Evaluation of sardine cohort growth operating model

The following notes document the results of applying a 6 year projection to Peter Kuriyama’s cohort growth Stock Synthesis model for Pacific sardine using {SSMSE}. The separate runs progress from a self test to applying additional sampling error in the SSMSE sampling module.

Self test with only acoustic-trawl index specified

# read in SSMSE results summary
tsSumry <- read.csv("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/results_ts_cohortGrowthselftest.csv")

# Get rid of duplicated SSB years
tsSumry <- na.omit(tsSumry)

# bring in simulated data for each iteration to plot with OM and EM vals
simDat <- data.frame()
for(i in c(2,4:9)){
  itDat <- SS_readdat(file = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/",
                           i, "/cohortGrowthOMandEM_EM_2024/data.ss_new"),
                      version = "3.30")[["CPUE"]] %>%
            filter(index == 4) %>%
            mutate(iteration = i,
                   model_run = "cohortGrowthselftest_data")

  simDat <- rbind(simDat, itDat)
}
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
# simDat <- SS_readdat(file = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024/data.ss_new",
#                       version = "3.30")[["CPUE"]] %>%
#             filter(index == 4) %>%
#             mutate(#iteration = i,
#                    model_run = "cohortGrowthselftest_data")

# plots of simulated and estimated biomass trends per iteration
ggplot2::ggplot(data = subset(tsSumry, model_run %in% c("0_estimate_cohort_growh_OM",  
                                                      "cohortGrowthOMandEM_EM_2020",
                                                      "cohortGrowthOMandEM_EM_2021",
                                                      "cohortGrowthOMandEM_EM_2022",
                                                      "cohortGrowthOMandEM_EM_2023",
                                                      "cohortGrowthOMandEM_EM_2024")), 
                ggplot2::aes(x = year, y = SpawnBio)) +
  ggplot2::geom_vline(xintercept = 2019, color = "gray") +
  geom_point(data = simDat, mapping = aes(x = year, y = obs), shape = 4, color = "grey") +
  ggplot2::geom_line(ggplot2::aes(linetype = as.character(iteration), color = model_run))+
  ggplot2::scale_color_manual(values = c("#D65F00", rep("black", 4), "blue")) +
  ggplot2::scale_linetype_manual(values = rep("solid", 50)) +
  ggplot2::guides(linetype = FALSE) +
  ggplot2::facet_wrap(. ~ iteration) +
  ggplot2::theme_classic()
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.

# plot of OM and EM and simulated data
indexPlot <- plot_index_sampling(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest")
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
# !!RW: sampled_dataset are different among iterations

indexPlot # !RW: only getting last three iterations, but gets the point across 
## $index_dat
##     year seas index        obs se_log iteration             scenario
## 1   2005   10     4 1947060.00  0.300         2 cohortGrowthselftest
## 2   2007   10     4  751075.00  0.090         2 cohortGrowthselftest
## 3   2009   10     4  357006.00  0.410         2 cohortGrowthselftest
## 4   2010   10     4  493672.00  0.300         2 cohortGrowthselftest
## 5   2011   10     4  469480.00  0.280         2 cohortGrowthselftest
## 6   2012   10     4  305146.00  0.240         2 cohortGrowthselftest
## 7   2013   10     4   35339.00  0.380         2 cohortGrowthselftest
## 8   2014   10     4   29048.00  0.290         2 cohortGrowthselftest
## 9   2015   10     4   83030.00  0.470         2 cohortGrowthselftest
## 10  2008    1     4  801000.00  0.300         2 cohortGrowthselftest
## 11  2012    1     4  340831.00  0.330         2 cohortGrowthselftest
## 12  2013    1     4  306191.00  0.293         2 cohortGrowthselftest
## 13  2014    1     4   26279.00  0.697         2 cohortGrowthselftest
## 14  2015    1     4   16375.00  0.940         2 cohortGrowthselftest
## 15  2016    1     4   72867.00  0.497         2 cohortGrowthselftest
## 16  2017    1     4   14103.00  0.300         2 cohortGrowthselftest
## 17  2018    1     4   25148.00  0.670         2 cohortGrowthselftest
## 18  2019    1     4   33632.00  0.190         2 cohortGrowthselftest
## 25  1986    1     5    4061.00  0.600         2 cohortGrowthselftest
## 26  1987    1     5    8661.00  0.560         2 cohortGrowthselftest
## 27  1993   10     5   69065.00  0.290         2 cohortGrowthselftest
## 28  2003   10     5  145274.00  0.230         2 cohortGrowthselftest
## 29  2004   10     5  459943.00  0.550         2 cohortGrowthselftest
## 30  2006   10     5  198404.00  0.300         2 cohortGrowthselftest
## 31  2007   10     5   66395.00  0.270         2 cohortGrowthselftest
## 32  2008   10     5   99162.00  0.240         2 cohortGrowthselftest
## 33  2009   10     5   58447.00  0.400         2 cohortGrowthselftest
## 34  2010   10     5  219386.00  0.270         2 cohortGrowthselftest
## 35  2011   10     5  113178.00  0.270         2 cohortGrowthselftest
## 36  2012   10     5   82182.00  0.290         2 cohortGrowthselftest
## 37  2014   10     5   19376.00  0.540         2 cohortGrowthselftest
## 38  1986    1     6   11220.00  0.730         2 cohortGrowthselftest
## 39  1987    1     6   25637.00  0.480         2 cohortGrowthselftest
## 40  1987   10     6   17266.00  0.350         2 cohortGrowthselftest
## 41  1993   10     6   73374.00  0.210         2 cohortGrowthselftest
## 42  1995   10     6   97923.00  0.400         2 cohortGrowthselftest
## 43  1996   10     6  482246.00  0.210         2 cohortGrowthselftest
## 44  1997   10     6  369775.00  0.330         2 cohortGrowthselftest
## 45  1998   10     6  332177.00  0.340         2 cohortGrowthselftest
## 46  1999   10     6 1252540.00  0.390         2 cohortGrowthselftest
## 47  2000   10     6  931377.00  0.380         2 cohortGrowthselftest
## 48  2001   10     6  236660.00  0.170         2 cohortGrowthselftest
## 49  2002   10     6  556177.00  0.180         2 cohortGrowthselftest
## 50  2003   10     6  307795.00  0.240         2 cohortGrowthselftest
## 51  2004   10     6  486950.00  0.400         2 cohortGrowthselftest
## 52  2005   10     6  651994.00  0.250         2 cohortGrowthselftest
## 53  2006   10     6  306297.00  0.260         2 cohortGrowthselftest
## 54  2007   10     6  128118.00  0.210         2 cohortGrowthselftest
## 55  2008   10     6  162188.00  0.220         2 cohortGrowthselftest
## 56  2009   10     6   97838.00  0.390         2 cohortGrowthselftest
## 57  2010   10     6  364798.00  0.260         2 cohortGrowthselftest
## 58  2011   10     6  227632.00  0.270         2 cohortGrowthselftest
## 59  2012   10     6  198472.00  0.290         2 cohortGrowthselftest
## 60  2014   10     6   30396.00  0.660         2 cohortGrowthselftest
## 61  2005   10     4 1101140.00  0.300         2 cohortGrowthselftest
## 62  2007   10     4  944250.00  0.090         2 cohortGrowthselftest
## 63  2009   10     4  485467.00  0.410         2 cohortGrowthselftest
## 64  2010   10     4  383976.00  0.300         2 cohortGrowthselftest
## 65  2011   10     4  370126.00  0.280         2 cohortGrowthselftest
## 66  2012   10     4  200798.00  0.240         2 cohortGrowthselftest
## 67  2013   10     4   84678.00  0.380         2 cohortGrowthselftest
## 68  2014   10     4   41015.20  0.290         2 cohortGrowthselftest
## 69  2015   10     4   40131.40  0.470         2 cohortGrowthselftest
## 70  2008    1     4  967167.00  0.300         2 cohortGrowthselftest
## 71  2012    1     4  348700.00  0.330         2 cohortGrowthselftest
## 72  2013    1     4  179274.00  0.293         2 cohortGrowthselftest
## 73  2014    1     4   76487.80  0.697         2 cohortGrowthselftest
## 74  2015    1     4   36195.70  0.940         2 cohortGrowthselftest
## 75  2016    1     4   43199.80  0.497         2 cohortGrowthselftest
## 76  2017    1     4   45528.50  0.300         2 cohortGrowthselftest
## 77  2018    1     4   41429.60  0.670         2 cohortGrowthselftest
## 78  2019    1     4   33218.90  0.190         2 cohortGrowthselftest
## 85  1986    1     5    4354.10  0.600         2 cohortGrowthselftest
## 86  1987    1     5    4891.42  0.560         2 cohortGrowthselftest
## 87  1993   10     5   26846.30  0.290         2 cohortGrowthselftest
## 88  2003   10     5   67235.50  0.230         2 cohortGrowthselftest
## 89  2004   10     5   80905.40  0.550         2 cohortGrowthselftest
## 90  2006   10     5  141476.00  0.300         2 cohortGrowthselftest
## 91  2007   10     5  133955.00  0.270         2 cohortGrowthselftest
## 92  2008   10     5  108731.00  0.240         2 cohortGrowthselftest
## 93  2009   10     5   76562.70  0.400         2 cohortGrowthselftest
## 94  2010   10     5   55439.30  0.270         2 cohortGrowthselftest
## 95  2011   10     5   55613.60  0.270         2 cohortGrowthselftest
## 96  2012   10     5   34929.00  0.290         2 cohortGrowthselftest
## 97  2014   10     5    7236.38  0.540         2 cohortGrowthselftest
## 98  1986    1     6   15046.10  0.730         2 cohortGrowthselftest
## 99  1987    1     6   16902.80  0.480         2 cohortGrowthselftest
## 100 1987   10     6   29702.40  0.350         2 cohortGrowthselftest
## 101 1993   10     6   92770.30  0.210         2 cohortGrowthselftest
## 102 1995   10     6  307084.00  0.400         2 cohortGrowthselftest
## 103 1996   10     6  443438.00  0.210         2 cohortGrowthselftest
## 104 1997   10     6  479106.00  0.330         2 cohortGrowthselftest
## 105 1998   10     6  497986.00  0.340         2 cohortGrowthselftest
## 106 1999   10     6  578660.00  0.390         2 cohortGrowthselftest
## 107 2000   10     6  556682.00  0.380         2 cohortGrowthselftest
## 108 2001   10     6  427305.00  0.170         2 cohortGrowthselftest
## 109 2002   10     6  328371.00  0.180         2 cohortGrowthselftest
## 110 2003   10     6  232340.00  0.240         2 cohortGrowthselftest
## 111 2004   10     6  279578.00  0.400         2 cohortGrowthselftest
## 112 2005   10     6  416060.00  0.250         2 cohortGrowthselftest
## 113 2006   10     6  488886.00  0.260         2 cohortGrowthselftest
## 114 2007   10     6  462898.00  0.210         2 cohortGrowthselftest
## 115 2008   10     6  375733.00  0.220         2 cohortGrowthselftest
## 116 2009   10     6  264571.00  0.390         2 cohortGrowthselftest
## 117 2010   10     6  191577.00  0.260         2 cohortGrowthselftest
## 118 2011   10     6  192179.00  0.270         2 cohortGrowthselftest
## 119 2012   10     6  120701.00  0.290         2 cohortGrowthselftest
## 120 2014   10     6   25006.10  0.660         2 cohortGrowthselftest
## 121 2005   10     4 1849260.00  0.300         2 cohortGrowthselftest
## 122 2007   10     4  736232.00  0.090         2 cohortGrowthselftest
## 123 2009   10     4  352322.00  0.410         2 cohortGrowthselftest
## 124 2010   10     4  369430.00  0.300         2 cohortGrowthselftest
## 125 2011   10     4  718850.00  0.280         2 cohortGrowthselftest
## 126 2012   10     4  273730.00  0.240         2 cohortGrowthselftest
## 127 2013   10     4   72283.40  0.380         2 cohortGrowthselftest
## 128 2014   10     4   66719.80  0.290         2 cohortGrowthselftest
## 129 2015   10     4   54881.80  0.470         2 cohortGrowthselftest
## 130 2008    1     4  783588.00  0.300         2 cohortGrowthselftest
## 131 2012    1     4  267836.00  0.330         2 cohortGrowthselftest
## 132 2013    1     4  166505.00  0.293         2 cohortGrowthselftest
## 133 2014    1     4   87074.70  0.697         2 cohortGrowthselftest
## 134 2015    1     4  156470.00  0.940         2 cohortGrowthselftest
## 135 2016    1     4   40421.80  0.497         2 cohortGrowthselftest
## 136 2017    1     4   64717.40  0.300         2 cohortGrowthselftest
## 137 2018    1     4   72090.70  0.670         2 cohortGrowthselftest
## 138 2019    1     4   36175.30  0.190         2 cohortGrowthselftest
## 139 1986    1     5    4687.39  0.600         2 cohortGrowthselftest
## 140 1987    1     5    6368.65  0.560         2 cohortGrowthselftest
## 141 1993   10     5   47161.60  0.290         2 cohortGrowthselftest
## 142 2003   10     5   57147.20  0.230         2 cohortGrowthselftest
## 143 2004   10     5  241352.00  0.550         2 cohortGrowthselftest
## 144 2006   10     5   94080.10  0.300         2 cohortGrowthselftest
## 145 2007   10     5  165026.00  0.270         2 cohortGrowthselftest
## 146 2008   10     5  100034.00  0.240         2 cohortGrowthselftest
## 147 2009   10     5   62249.20  0.400         2 cohortGrowthselftest
## 148 2010   10     5   62577.90  0.270         2 cohortGrowthselftest
## 149 2011   10     5   47105.10  0.270         2 cohortGrowthselftest
## 150 2012   10     5   33411.70  0.290         2 cohortGrowthselftest
## 151 2014   10     5   21391.10  0.540         2 cohortGrowthselftest
## 152 1986    1     6    7264.25  0.730         2 cohortGrowthselftest
## 153 1987    1     6   25226.50  0.480         2 cohortGrowthselftest
## 154 1987   10     6   33161.60  0.350         2 cohortGrowthselftest
## 155 1993   10     6  126418.00  0.210         2 cohortGrowthselftest
## 156 1995   10     6  235376.00  0.400         2 cohortGrowthselftest
## 157 1996   10     6  371177.00  0.210         2 cohortGrowthselftest
## 158 1997   10     6  681632.00  0.330         2 cohortGrowthselftest
## 159 1998   10     6  773135.00  0.340         2 cohortGrowthselftest
## 160 1999   10     6  515309.00  0.390         2 cohortGrowthselftest
## 161 2000   10     6  688020.00  0.380         2 cohortGrowthselftest
## 162 2001   10     6  377793.00  0.170         2 cohortGrowthselftest
## 163 2002   10     6  324992.00  0.180         2 cohortGrowthselftest
## 164 2003   10     6  148135.00  0.240         2 cohortGrowthselftest
## 165 2004   10     6  670079.00  0.400         2 cohortGrowthselftest
## 166 2005   10     6  350421.00  0.250         2 cohortGrowthselftest
## 167 2006   10     6  630179.00  0.260         2 cohortGrowthselftest
## 168 2007   10     6  267310.00  0.210         2 cohortGrowthselftest
## 169 2008   10     6  378205.00  0.220         2 cohortGrowthselftest
## 170 2009   10     6  201204.00  0.390         2 cohortGrowthselftest
## 171 2010   10     6  208797.00  0.260         2 cohortGrowthselftest
## 172 2011   10     6  225686.00  0.270         2 cohortGrowthselftest
## 173 2012   10     6   87803.90  0.290         2 cohortGrowthselftest
## 174 2014   10     6   24344.90  0.660         2 cohortGrowthselftest
## 175 2005   10     4 1273580.00  0.300         4 cohortGrowthselftest
## 176 2007   10     4  956795.00  0.090         4 cohortGrowthselftest
## 177 2009   10     4  833354.00  0.410         4 cohortGrowthselftest
## 178 2010   10     4  329810.00  0.300         4 cohortGrowthselftest
## 179 2011   10     4  328997.00  0.280         4 cohortGrowthselftest
## 180 2012   10     4  188288.00  0.240         4 cohortGrowthselftest
## 181 2013   10     4   45838.30  0.380         4 cohortGrowthselftest
## 182 2014   10     4   47527.60  0.290         4 cohortGrowthselftest
## 183 2015   10     4   66378.60  0.470         4 cohortGrowthselftest
## 184 2008    1     4 1095470.00  0.300         4 cohortGrowthselftest
## 185 2012    1     4  319878.00  0.330         4 cohortGrowthselftest
## 186 2013    1     4  146493.00  0.293         4 cohortGrowthselftest
## 187 2014    1     4   80463.80  0.697         4 cohortGrowthselftest
## 188 2015    1     4   60785.50  0.940         4 cohortGrowthselftest
## 189 2016    1     4   83395.40  0.497         4 cohortGrowthselftest
## 190 2017    1     4   63344.30  0.300         4 cohortGrowthselftest
## 191 2018    1     4   27301.00  0.670         4 cohortGrowthselftest
## 192 2019    1     4   31728.10  0.190         4 cohortGrowthselftest
## 193 1986    1     5    1840.14  0.600         4 cohortGrowthselftest
## 194 1987    1     5   12034.40  0.560         4 cohortGrowthselftest
## 195 1993   10     5   24993.50  0.290         4 cohortGrowthselftest
## 196 2003   10     5   61183.10  0.230         4 cohortGrowthselftest
## 197 2004   10     5   85559.70  0.550         4 cohortGrowthselftest
## 198 2006   10     5  173592.00  0.300         4 cohortGrowthselftest
## 199 2007   10     5  107337.00  0.270         4 cohortGrowthselftest
## 200 2008   10     5  191128.00  0.240         4 cohortGrowthselftest
## 201 2009   10     5  107944.00  0.400         4 cohortGrowthselftest
## 202 2010   10     5   45362.60  0.270         4 cohortGrowthselftest
## 203 2011   10     5   80481.20  0.270         4 cohortGrowthselftest
## 204 2012   10     5   33414.40  0.290         4 cohortGrowthselftest
## 205 2014   10     5   19364.10  0.540         4 cohortGrowthselftest
## 206 1986    1     6   17133.10  0.730         4 cohortGrowthselftest
## 207 1987    1     6   12026.10  0.480         4 cohortGrowthselftest
## 208 1987   10     6   29926.30  0.350         4 cohortGrowthselftest
## 209 1993   10     6   89433.50  0.210         4 cohortGrowthselftest
## 210 1995   10     6  214749.00  0.400         4 cohortGrowthselftest
## 211 1996   10     6  416808.00  0.210         4 cohortGrowthselftest
## 212 1997   10     6  760750.00  0.330         4 cohortGrowthselftest
## 213 1998   10     6  513017.00  0.340         4 cohortGrowthselftest
## 214 1999   10     6  620087.00  0.390         4 cohortGrowthselftest
## 215 2000   10     6 1207500.00  0.380         4 cohortGrowthselftest
## 216 2001   10     6  638326.00  0.170         4 cohortGrowthselftest
## 217 2002   10     6  283222.00  0.180         4 cohortGrowthselftest
## 218 2003   10     6  223028.00  0.240         4 cohortGrowthselftest
## 219 2004   10     6  201695.00  0.400         4 cohortGrowthselftest
## 220 2005   10     6  594578.00  0.250         4 cohortGrowthselftest
## 221 2006   10     6  420836.00  0.260         4 cohortGrowthselftest
## 222 2007   10     6  448229.00  0.210         4 cohortGrowthselftest
## 223 2008   10     6  342041.00  0.220         4 cohortGrowthselftest
## 224 2009   10     6  292266.00  0.390         4 cohortGrowthselftest
## 225 2010   10     6  217327.00  0.260         4 cohortGrowthselftest
## 226 2011   10     6  186836.00  0.270         4 cohortGrowthselftest
## 227 2012   10     6  121746.00  0.290         4 cohortGrowthselftest
## 228 2014   10     6   91560.10  0.660         4 cohortGrowthselftest
## 229 2005   10     4 1236650.00  0.300         5 cohortGrowthselftest
## 230 2007   10     4 1052950.00  0.090         5 cohortGrowthselftest
## 231 2009   10     4  273910.00  0.410         5 cohortGrowthselftest
## 232 2010   10     4  397137.00  0.300         5 cohortGrowthselftest
## 233 2011   10     4  481964.00  0.280         5 cohortGrowthselftest
## 234 2012   10     4  228273.00  0.240         5 cohortGrowthselftest
## 235 2013   10     4   54517.10  0.380         5 cohortGrowthselftest
## 236 2014   10     4   81714.60  0.290         5 cohortGrowthselftest
## 237 2015   10     4   15419.10  0.470         5 cohortGrowthselftest
## 238 2008    1     4  908212.00  0.300         5 cohortGrowthselftest
## 239 2012    1     4  222648.00  0.330         5 cohortGrowthselftest
## 240 2013    1     4  152144.00  0.293         5 cohortGrowthselftest
## 241 2014    1     4   70841.50  0.697         5 cohortGrowthselftest
## 242 2015    1     4   23057.30  0.940         5 cohortGrowthselftest
## 243 2016    1     4   30705.80  0.497         5 cohortGrowthselftest
## 244 2017    1     4   45924.20  0.300         5 cohortGrowthselftest
## 245 2018    1     4   41260.60  0.670         5 cohortGrowthselftest
## 246 2019    1     4   36906.20  0.190         5 cohortGrowthselftest
## 247 1986    1     5    8131.22  0.600         5 cohortGrowthselftest
## 248 1987    1     5    2430.50  0.560         5 cohortGrowthselftest
## 249 1993   10     5   23324.90  0.290         5 cohortGrowthselftest
## 250 2003   10     5   58452.20  0.230         5 cohortGrowthselftest
## 251 2004   10     5   65035.40  0.550         5 cohortGrowthselftest
## 252 2006   10     5  109329.00  0.300         5 cohortGrowthselftest
## 253 2007   10     5  154467.00  0.270         5 cohortGrowthselftest
## 254 2008   10     5   68056.30  0.240         5 cohortGrowthselftest
## 255 2009   10     5   72360.30  0.400         5 cohortGrowthselftest
## 256 2010   10     5   44703.20  0.270         5 cohortGrowthselftest
## 257 2011   10     5   54234.90  0.270         5 cohortGrowthselftest
## 258 2012   10     5   32600.60  0.290         5 cohortGrowthselftest
## 259 2014   10     5    3775.21  0.540         5 cohortGrowthselftest
## 260 1986    1     6   18676.60  0.730         5 cohortGrowthselftest
## 261 1987    1     6   19940.10  0.480         5 cohortGrowthselftest
## 262 1987   10     6   29682.60  0.350         5 cohortGrowthselftest
## 263 1993   10     6   69470.00  0.210         5 cohortGrowthselftest
## 264 1995   10     6  392947.00  0.400         5 cohortGrowthselftest
## 265 1996   10     6  370045.00  0.210         5 cohortGrowthselftest
## 266 1997   10     6  546270.00  0.330         5 cohortGrowthselftest
## 267 1998   10     6  321022.00  0.340         5 cohortGrowthselftest
## 268 1999   10     6  633369.00  0.390         5 cohortGrowthselftest
## 269 2000   10     6  583315.00  0.380         5 cohortGrowthselftest
## 270 2001   10     6  418106.00  0.170         5 cohortGrowthselftest
## 271 2002   10     6  373917.00  0.180         5 cohortGrowthselftest
## 272 2003   10     6  253238.00  0.240         5 cohortGrowthselftest
## 273 2004   10     6  274313.00  0.400         5 cohortGrowthselftest
## 274 2005   10     6  434194.00  0.250         5 cohortGrowthselftest
## 275 2006   10     6  524170.00  0.260         5 cohortGrowthselftest
## 276 2007   10     6  281360.00  0.210         5 cohortGrowthselftest
## 277 2008   10     6  645590.00  0.220         5 cohortGrowthselftest
## 278 2009   10     6  540859.00  0.390         5 cohortGrowthselftest
## 279 2010   10     6  128197.00  0.260         5 cohortGrowthselftest
## 280 2011   10     6  169739.00  0.270         5 cohortGrowthselftest
## 281 2012   10     6   76649.00  0.290         5 cohortGrowthselftest
## 282 2014   10     6   22410.20  0.660         5 cohortGrowthselftest
## 283 2005   10     4 1715810.00  0.300         6 cohortGrowthselftest
## 284 2007   10     4  903193.00  0.090         6 cohortGrowthselftest
## 285 2009   10     4  566609.00  0.410         6 cohortGrowthselftest
## 286 2010   10     4  537752.00  0.300         6 cohortGrowthselftest
## 287 2011   10     4  269894.00  0.280         6 cohortGrowthselftest
## 288 2012   10     4  189472.00  0.240         6 cohortGrowthselftest
## 289 2013   10     4   57437.10  0.380         6 cohortGrowthselftest
## 290 2014   10     4   44603.00  0.290         6 cohortGrowthselftest
## 291 2015   10     4   64365.80  0.470         6 cohortGrowthselftest
## 292 2008    1     4  853675.00  0.300         6 cohortGrowthselftest
## 293 2012    1     4  342219.00  0.330         6 cohortGrowthselftest
## 294 2013    1     4  354352.00  0.293         6 cohortGrowthselftest
## 295 2014    1     4  204476.00  0.697         6 cohortGrowthselftest
## 296 2015    1     4  110309.00  0.940         6 cohortGrowthselftest
## 297 2016    1     4   27838.30  0.497         6 cohortGrowthselftest
## 298 2017    1     4   43216.30  0.300         6 cohortGrowthselftest
## 299 2018    1     4   41334.70  0.670         6 cohortGrowthselftest
## 300 2019    1     4   35617.50  0.190         6 cohortGrowthselftest
## 301 1986    1     5    8849.26  0.600         6 cohortGrowthselftest
## 302 1987    1     5    6175.15  0.560         6 cohortGrowthselftest
## 303 1993   10     5   36462.70  0.290         6 cohortGrowthselftest
## 304 2003   10     5   84163.10  0.230         6 cohortGrowthselftest
## 305 2004   10     5  129617.00  0.550         6 cohortGrowthselftest
## 306 2006   10     5  130025.00  0.300         6 cohortGrowthselftest
## 307 2007   10     5  178531.00  0.270         6 cohortGrowthselftest
## 308 2008   10     5  172268.00  0.240         6 cohortGrowthselftest
## 309 2009   10     5  102699.00  0.400         6 cohortGrowthselftest
## 310 2010   10     5   76853.40  0.270         6 cohortGrowthselftest
## 311 2011   10     5   59295.60  0.270         6 cohortGrowthselftest
## 312 2012   10     5   27173.80  0.290         6 cohortGrowthselftest
## 313 2014   10     5    8168.78  0.540         6 cohortGrowthselftest
## 314 1986    1     6   39912.50  0.730         6 cohortGrowthselftest
## 315 1987    1     6   24540.20  0.480         6 cohortGrowthselftest
## 316 1987   10     6   19631.60  0.350         6 cohortGrowthselftest
## 317 1993   10     6  116456.00  0.210         6 cohortGrowthselftest
## 318 1995   10     6  321291.00  0.400         6 cohortGrowthselftest
## 319 1996   10     6  265594.00  0.210         6 cohortGrowthselftest
## 320 1997   10     6  397998.00  0.330         6 cohortGrowthselftest
## 321 1998   10     6  539604.00  0.340         6 cohortGrowthselftest
## 322 1999   10     6  629355.00  0.390         6 cohortGrowthselftest
## 323 2000   10     6  543633.00  0.380         6 cohortGrowthselftest
## 324 2001   10     6  351253.00  0.170         6 cohortGrowthselftest
## 325 2002   10     6  401143.00  0.180         6 cohortGrowthselftest
## 326 2003   10     6  332752.00  0.240         6 cohortGrowthselftest
## 327 2004   10     6  434401.00  0.400         6 cohortGrowthselftest
## 328 2005   10     6  473800.00  0.250         6 cohortGrowthselftest
## 329 2006   10     6  509759.00  0.260         6 cohortGrowthselftest
## 330 2007   10     6  453935.00  0.210         6 cohortGrowthselftest
## 331 2008   10     6  437798.00  0.220         6 cohortGrowthselftest
## 332 2009   10     6  310228.00  0.390         6 cohortGrowthselftest
## 333 2010   10     6  237757.00  0.260         6 cohortGrowthselftest
## 334 2011   10     6  218337.00  0.270         6 cohortGrowthselftest
## 335 2012   10     6   97585.90  0.290         6 cohortGrowthselftest
## 336 2014   10     6   35344.20  0.660         6 cohortGrowthselftest
## 337 2005   10     4  809070.00  0.300         7 cohortGrowthselftest
## 338 2007   10     4  984829.00  0.090         7 cohortGrowthselftest
## 339 2009   10     4  617036.00  0.410         7 cohortGrowthselftest
## 340 2010   10     4  358310.00  0.300         7 cohortGrowthselftest
## 341 2011   10     4  504825.00  0.280         7 cohortGrowthselftest
## 342 2012   10     4  210589.00  0.240         7 cohortGrowthselftest
## 343 2013   10     4   68530.40  0.380         7 cohortGrowthselftest
## 344 2014   10     4   66526.00  0.290         7 cohortGrowthselftest
## 345 2015   10     4   17234.90  0.470         7 cohortGrowthselftest
## 346 2008    1     4  935789.00  0.300         7 cohortGrowthselftest
## 347 2012    1     4  435753.00  0.330         7 cohortGrowthselftest
## 348 2013    1     4  215050.00  0.293         7 cohortGrowthselftest
## 349 2014    1     4  174268.00  0.697         7 cohortGrowthselftest
## 350 2015    1     4   78982.30  0.940         7 cohortGrowthselftest
## 351 2016    1     4   11955.70  0.497         7 cohortGrowthselftest
## 352 2017    1     4   39469.00  0.300         7 cohortGrowthselftest
## 353 2018    1     4   28599.00  0.670         7 cohortGrowthselftest
## 354 2019    1     4   39239.40  0.190         7 cohortGrowthselftest
## 355 1986    1     5    3224.00  0.600         7 cohortGrowthselftest
## 356 1987    1     5    2087.72  0.560         7 cohortGrowthselftest
## 357 1993   10     5   38552.60  0.290         7 cohortGrowthselftest
## 358 2003   10     5   85270.50  0.230         7 cohortGrowthselftest
## 359 2004   10     5   71704.70  0.550         7 cohortGrowthselftest
## 360 2006   10     5  134151.00  0.300         7 cohortGrowthselftest
## 361 2007   10     5  110034.00  0.270         7 cohortGrowthselftest
## 362 2008   10     5  136620.00  0.240         7 cohortGrowthselftest
## 363 2009   10     5   73130.20  0.400         7 cohortGrowthselftest
## 364 2010   10     5   50762.20  0.270         7 cohortGrowthselftest
## 365 2011   10     5   50474.00  0.270         7 cohortGrowthselftest
## 366 2012   10     5   34888.30  0.290         7 cohortGrowthselftest
## 367 2014   10     5    6286.22  0.540         7 cohortGrowthselftest
## 368 1986    1     6   20503.00  0.730         7 cohortGrowthselftest
## 369 1987    1     6   27461.90  0.480         7 cohortGrowthselftest
## 370 1987   10     6   35026.90  0.350         7 cohortGrowthselftest
## 371 1993   10     6  131919.00  0.210         7 cohortGrowthselftest
## 372 1995   10     6  212092.00  0.400         7 cohortGrowthselftest
## 373 1996   10     6  487677.00  0.210         7 cohortGrowthselftest
## 374 1997   10     6  425824.00  0.330         7 cohortGrowthselftest
## 375 1998   10     6 1454620.00  0.340         7 cohortGrowthselftest
## 376 1999   10     6  756531.00  0.390         7 cohortGrowthselftest
## 377 2000   10     6 1140470.00  0.380         7 cohortGrowthselftest
## 378 2001   10     6  406106.00  0.170         7 cohortGrowthselftest
## 379 2002   10     6  323548.00  0.180         7 cohortGrowthselftest
## 380 2003   10     6  455874.00  0.240         7 cohortGrowthselftest
## 381 2004   10     6  169939.00  0.400         7 cohortGrowthselftest
## 382 2005   10     6  390169.00  0.250         7 cohortGrowthselftest
## 383 2006   10     6  721717.00  0.260         7 cohortGrowthselftest
## 384 2007   10     6  259102.00  0.210         7 cohortGrowthselftest
## 385 2008   10     6  330947.00  0.220         7 cohortGrowthselftest
## 386 2009   10     6  171863.00  0.390         7 cohortGrowthselftest
## 387 2010   10     6  233285.00  0.260         7 cohortGrowthselftest
## 388 2011   10     6  205884.00  0.270         7 cohortGrowthselftest
## 389 2012   10     6   92035.90  0.290         7 cohortGrowthselftest
## 390 2014   10     6   28706.70  0.660         7 cohortGrowthselftest
## 391 2005   10     4 1175170.00  0.300         8 cohortGrowthselftest
## 392 2007   10     4  874505.00  0.090         8 cohortGrowthselftest
## 393 2009   10     4  257698.00  0.410         8 cohortGrowthselftest
## 394 2010   10     4  483967.00  0.300         8 cohortGrowthselftest
## 395 2011   10     4  379795.00  0.280         8 cohortGrowthselftest
## 396 2012   10     4  235197.00  0.240         8 cohortGrowthselftest
## 397 2013   10     4  129553.00  0.380         8 cohortGrowthselftest
## 398 2014   10     4   31636.20  0.290         8 cohortGrowthselftest
## 399 2015   10     4   19465.10  0.470         8 cohortGrowthselftest
## 400 2008    1     4  624801.00  0.300         8 cohortGrowthselftest
## 401 2012    1     4  254300.00  0.330         8 cohortGrowthselftest
## 402 2013    1     4  206454.00  0.293         8 cohortGrowthselftest
## 403 2014    1     4   85902.50  0.697         8 cohortGrowthselftest
## 404 2015    1     4   63890.80  0.940         8 cohortGrowthselftest
## 405 2016    1     4  106199.00  0.497         8 cohortGrowthselftest
## 406 2017    1     4   46967.50  0.300         8 cohortGrowthselftest
## 407 2018    1     4   23569.10  0.670         8 cohortGrowthselftest
## 408 2019    1     4   36855.80  0.190         8 cohortGrowthselftest
## 409 1986    1     5    3709.67  0.600         8 cohortGrowthselftest
## 410 1987    1     5    5505.26  0.560         8 cohortGrowthselftest
## 411 1993   10     5   30049.40  0.290         8 cohortGrowthselftest
## 412 2003   10     5   66770.20  0.230         8 cohortGrowthselftest
## 413 2004   10     5   80911.40  0.550         8 cohortGrowthselftest
## 414 2006   10     5  272475.00  0.300         8 cohortGrowthselftest
## 415 2007   10     5  171586.00  0.270         8 cohortGrowthselftest
## 416 2008   10     5  120646.00  0.240         8 cohortGrowthselftest
## 417 2009   10     5   55773.00  0.400         8 cohortGrowthselftest
## 418 2010   10     5   64527.60  0.270         8 cohortGrowthselftest
## 419 2011   10     5   83034.30  0.270         8 cohortGrowthselftest
## 420 2012   10     5   31008.00  0.290         8 cohortGrowthselftest
## 421 2014   10     5    4191.42  0.540         8 cohortGrowthselftest
## 422 1986    1     6   44622.10  0.730         8 cohortGrowthselftest
## 423 1987    1     6   14814.80  0.480         8 cohortGrowthselftest
## 424 1987   10     6   48390.80  0.350         8 cohortGrowthselftest
## 425 1993   10     6   89041.90  0.210         8 cohortGrowthselftest
## 426 1995   10     6  331478.00  0.400         8 cohortGrowthselftest
## 427 1996   10     6  449873.00  0.210         8 cohortGrowthselftest
## 428 1997   10     6  558446.00  0.330         8 cohortGrowthselftest
## 429 1998   10     6  831350.00  0.340         8 cohortGrowthselftest
## 430 1999   10     6  552492.00  0.390         8 cohortGrowthselftest
## 431 2000   10     6  341350.00  0.380         8 cohortGrowthselftest
## 432 2001   10     6  511001.00  0.170         8 cohortGrowthselftest
## 433 2002   10     6  331949.00  0.180         8 cohortGrowthselftest
## 434 2003   10     6  235632.00  0.240         8 cohortGrowthselftest
## 435 2004   10     6  233135.00  0.400         8 cohortGrowthselftest
## 436 2005   10     6  396254.00  0.250         8 cohortGrowthselftest
## 437 2006   10     6  290096.00  0.260         8 cohortGrowthselftest
## 438 2007   10     6  474052.00  0.210         8 cohortGrowthselftest
## 439 2008   10     6  459917.00  0.220         8 cohortGrowthselftest
## 440 2009   10     6  232746.00  0.390         8 cohortGrowthselftest
## 441 2010   10     6  218156.00  0.260         8 cohortGrowthselftest
## 442 2011   10     6  217456.00  0.270         8 cohortGrowthselftest
## 443 2012   10     6  179588.00  0.290         8 cohortGrowthselftest
## 444 2014   10     6   25992.60  0.660         8 cohortGrowthselftest
## 445 2005   10     4 1852970.00  0.300         9 cohortGrowthselftest
## 446 2007   10     4  921944.00  0.090         9 cohortGrowthselftest
## 447 2009   10     4  900777.00  0.410         9 cohortGrowthselftest
## 448 2010   10     4  401490.00  0.300         9 cohortGrowthselftest
## 449 2011   10     4  303678.00  0.280         9 cohortGrowthselftest
## 450 2012   10     4  278312.00  0.240         9 cohortGrowthselftest
## 451 2013   10     4   75216.90  0.380         9 cohortGrowthselftest
## 452 2014   10     4   37193.10  0.290         9 cohortGrowthselftest
## 453 2015   10     4   28392.80  0.470         9 cohortGrowthselftest
## 454 2008    1     4  835181.00  0.300         9 cohortGrowthselftest
## 455 2012    1     4  327496.00  0.330         9 cohortGrowthselftest
## 456 2013    1     4  116319.00  0.293         9 cohortGrowthselftest
## 457 2014    1     4   72099.10  0.697         9 cohortGrowthselftest
## 458 2015    1     4   14457.10  0.940         9 cohortGrowthselftest
## 459 2016    1     4   45758.70  0.497         9 cohortGrowthselftest
## 460 2017    1     4   49649.20  0.300         9 cohortGrowthselftest
## 461 2018    1     4   25492.20  0.670         9 cohortGrowthselftest
## 462 2019    1     4   35059.30  0.190         9 cohortGrowthselftest
## 463 1986    1     5   13631.90  0.600         9 cohortGrowthselftest
## 464 1987    1     5    2708.64  0.560         9 cohortGrowthselftest
## 465 1993   10     5   34501.40  0.290         9 cohortGrowthselftest
## 466 2003   10     5   85930.50  0.230         9 cohortGrowthselftest
## 467 2004   10     5  131636.00  0.550         9 cohortGrowthselftest
## 468 2006   10     5  151099.00  0.300         9 cohortGrowthselftest
## 469 2007   10     5  109194.00  0.270         9 cohortGrowthselftest
## 470 2008   10     5  150091.00  0.240         9 cohortGrowthselftest
## 471 2009   10     5  112830.00  0.400         9 cohortGrowthselftest
## 472 2010   10     5   48127.70  0.270         9 cohortGrowthselftest
## 473 2011   10     5   50786.80  0.270         9 cohortGrowthselftest
## 474 2012   10     5   26183.50  0.290         9 cohortGrowthselftest
## 475 2014   10     5   19361.40  0.540         9 cohortGrowthselftest
## 476 1986    1     6   35177.70  0.730         9 cohortGrowthselftest
## 477 1987    1     6   20273.00  0.480         9 cohortGrowthselftest
## 478 1987   10     6   22073.00  0.350         9 cohortGrowthselftest
## 479 1993   10     6   97742.70  0.210         9 cohortGrowthselftest
## 480 1995   10     6  190614.00  0.400         9 cohortGrowthselftest
## 481 1996   10     6  586025.00  0.210         9 cohortGrowthselftest
## 482 1997   10     6  416900.00  0.330         9 cohortGrowthselftest
## 483 1998   10     6  480223.00  0.340         9 cohortGrowthselftest
## 484 1999   10     6  699698.00  0.390         9 cohortGrowthselftest
## 485 2000   10     6  348349.00  0.380         9 cohortGrowthselftest
## 486 2001   10     6  516666.00  0.170         9 cohortGrowthselftest
## 487 2002   10     6  328623.00  0.180         9 cohortGrowthselftest
## 488 2003   10     6  280141.00  0.240         9 cohortGrowthselftest
## 489 2004   10     6  276025.00  0.400         9 cohortGrowthselftest
## 490 2005   10     6  254271.00  0.250         9 cohortGrowthselftest
## 491 2006   10     6  476442.00  0.260         9 cohortGrowthselftest
## 492 2007   10     6  544301.00  0.210         9 cohortGrowthselftest
## 493 2008   10     6  290753.00  0.220         9 cohortGrowthselftest
## 494 2009   10     6  215718.00  0.390         9 cohortGrowthselftest
## 495 2010   10     6  388838.00  0.260         9 cohortGrowthselftest
## 496 2011   10     6  223064.00  0.270         9 cohortGrowthselftest
## 497 2012   10     6  134823.00  0.290         9 cohortGrowthselftest
## 498 2014   10     6   97158.10  0.660         9 cohortGrowthselftest
##              model_run
## 1    historical_values
## 2    historical_values
## 3    historical_values
## 4    historical_values
## 5    historical_values
## 6    historical_values
## 7    historical_values
## 8    historical_values
## 9    historical_values
## 10   historical_values
## 11   historical_values
## 12   historical_values
## 13   historical_values
## 14   historical_values
## 15   historical_values
## 16   historical_values
## 17   historical_values
## 18   historical_values
## 25   historical_values
## 26   historical_values
## 27   historical_values
## 28   historical_values
## 29   historical_values
## 30   historical_values
## 31   historical_values
## 32   historical_values
## 33   historical_values
## 34   historical_values
## 35   historical_values
## 36   historical_values
## 37   historical_values
## 38   historical_values
## 39   historical_values
## 40   historical_values
## 41   historical_values
## 42   historical_values
## 43   historical_values
## 44   historical_values
## 45   historical_values
## 46   historical_values
## 47   historical_values
## 48   historical_values
## 49   historical_values
## 50   historical_values
## 51   historical_values
## 52   historical_values
## 53   historical_values
## 54   historical_values
## 55   historical_values
## 56   historical_values
## 57   historical_values
## 58   historical_values
## 59   historical_values
## 60   historical_values
## 61  OM_expected_values
## 62  OM_expected_values
## 63  OM_expected_values
## 64  OM_expected_values
## 65  OM_expected_values
## 66  OM_expected_values
## 67  OM_expected_values
## 68  OM_expected_values
## 69  OM_expected_values
## 70  OM_expected_values
## 71  OM_expected_values
## 72  OM_expected_values
## 73  OM_expected_values
## 74  OM_expected_values
## 75  OM_expected_values
## 76  OM_expected_values
## 77  OM_expected_values
## 78  OM_expected_values
## 85  OM_expected_values
## 86  OM_expected_values
## 87  OM_expected_values
## 88  OM_expected_values
## 89  OM_expected_values
## 90  OM_expected_values
## 91  OM_expected_values
## 92  OM_expected_values
## 93  OM_expected_values
## 94  OM_expected_values
## 95  OM_expected_values
## 96  OM_expected_values
## 97  OM_expected_values
## 98  OM_expected_values
## 99  OM_expected_values
## 100 OM_expected_values
## 101 OM_expected_values
## 102 OM_expected_values
## 103 OM_expected_values
## 104 OM_expected_values
## 105 OM_expected_values
## 106 OM_expected_values
## 107 OM_expected_values
## 108 OM_expected_values
## 109 OM_expected_values
## 110 OM_expected_values
## 111 OM_expected_values
## 112 OM_expected_values
## 113 OM_expected_values
## 114 OM_expected_values
## 115 OM_expected_values
## 116 OM_expected_values
## 117 OM_expected_values
## 118 OM_expected_values
## 119 OM_expected_values
## 120 OM_expected_values
## 121    sampled_dataset
## 122    sampled_dataset
## 123    sampled_dataset
## 124    sampled_dataset
## 125    sampled_dataset
## 126    sampled_dataset
## 127    sampled_dataset
## 128    sampled_dataset
## 129    sampled_dataset
## 130    sampled_dataset
## 131    sampled_dataset
## 132    sampled_dataset
## 133    sampled_dataset
## 134    sampled_dataset
## 135    sampled_dataset
## 136    sampled_dataset
## 137    sampled_dataset
## 138    sampled_dataset
## 139    sampled_dataset
## 140    sampled_dataset
## 141    sampled_dataset
## 142    sampled_dataset
## 143    sampled_dataset
## 144    sampled_dataset
## 145    sampled_dataset
## 146    sampled_dataset
## 147    sampled_dataset
## 148    sampled_dataset
## 149    sampled_dataset
## 150    sampled_dataset
## 151    sampled_dataset
## 152    sampled_dataset
## 153    sampled_dataset
## 154    sampled_dataset
## 155    sampled_dataset
## 156    sampled_dataset
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## 
## $index_plot

Summary plots of terminal year estimates

termYr <- tsSumry %>% filter(model_run %in% c("0_estimate_cohort_growh_OM", 
                                              "cohortGrowthOMandEM_EM_init") | # or keep end years
                             year == as.numeric(regmatches(model_run, 
                                                           gregexpr("[[:digit:]]+", model_run))))

termYr <- termYr %>% mutate(model_run = as.character(model_run),
                            model_run = case_when(!model_run %in% c("0_estimate_cohort_growh_OM", 
                                                                    "cohortGrowthOMandEM_EM_init") ~"cohortGrowthOMandEM_EM_term",
                                                  TRUE ~ model_run))

ggplot2::ggplot(data = termYr, 
                ggplot2::aes(x = year, y = SpawnBio)) +
  ggplot2::geom_vline(xintercept = 2019, color = "gray") +
  geom_point(data = simDat, mapping = aes(x = year, y = obs), shape = 4, color = "grey") +
  ggplot2::geom_line(ggplot2::aes(linetype = as.character(iteration), color = model_run))+
  ggplot2::scale_color_manual(values = c("#D65F00", "black", rep("blue", 5))) +
  ggplot2::scale_linetype_manual(values = rep("solid", 50)) +
  ggplot2::guides(linetype = FALSE) +
  ggplot2::facet_wrap(. ~ iteration) +
  ggplot2::theme_classic()
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.

relSSB_EMtoOM <- termYr %>% select(model_run, year, iteration, SpawnBio) %>%
                    pivot_wider(id_cols = c(year, iteration),
                                names_from = model_run, values_from = SpawnBio) %>%
                    rename(cohort_growth_OM = "0_estimate_cohort_growh_OM") %>%
                    mutate(diffSSB = case_when(is.na(cohortGrowthOMandEM_EM_term) ~ cohortGrowthOMandEM_EM_init - cohort_growth_OM,
                                               !is.na(cohortGrowthOMandEM_EM_term) ~ cohortGrowthOMandEM_EM_term - cohort_growth_OM))

relSSB_EMtoOM <- relSSB_EMtoOM %>% full_join(y = simDat, by = c("year", "iteration")) %>%
                    mutate(diffDat = obs - cohort_growth_OM)

ggplot(data = relSSB_EMtoOM, aes(x = year, y = diffSSB)) +
  ggplot2::geom_vline(xintercept = 2019, color = "gray") +
  geom_hline(yintercept = 0, color = "black") +
  geom_point(mapping = aes(x = year, y = diffDat), shape = 4, color = "grey") +
  ggplot2::geom_line(ggplot2::aes(linetype = as.character(iteration), color = 2))+
  #ggplot2::scale_color_manual(values = c("#D65F00", "black", rep("blue", 5))) +
  ggplot2::scale_linetype_manual(values = rep("solid", 50)) +
  ggplot2::guides(linetype = FALSE) +
  ggplot2::facet_wrap(. ~ iteration) +
  ggplot2::theme_classic()
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## Warning: Removed 182 rows containing missing values (geom_point).
## Warning: Removed 7 row(s) containing missing values (geom_path).

Plots of length and age composition

# plot_comp_sampling(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest", comp_type = "agecomp")
# !!!Error: The comp database from the operating model has no rows, so must not have been any historical data in the OM.

outputSS <- SS_output(
  dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024",
  dir.mcmc = NULL,
  repfile = "Report.sso",
  compfile = "CompReport.sso")
## Getting header info from:
##   C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024/Report.sso
## This function tested on SS versions 3.24 and 3.30.
##   You are using 3.30.16.00 which SHOULD work with this package.
## Report file time:Wed Jul 21 10:33:46 2021
## Warning in SS_output(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024", : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Reading full report file
## Got all columns using ncols = 62
## Got Report file
## Setting minimum biomass threshhold to 0.25  based on US west coast assumption associated with biomass target of 0.4.  (can replace or override in SS_plots by setting 'minbthresh')
## No non-empty log file in directory or too many files  matching pattern *.log
## Got warning file. Therewere 8 warnings in C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024/warning.sso
## Finished reading files
## CompReport file separated by this code as follows (rows = Ncomps*Nbins):
##   3510 rows of length comp data,
##   0 rows of generalized size comp data,
##   0 rows of age comp data,
##   8991 rows of conditional age-at-length data,
##   783 rows of ghost fleet age comp data,
##   0 rows of ghost fleet conditional age-at-length data,
##   468 rows of ghost fleet length comp data,
##   0 rows of mean length at age data,
##   0 rows of mean weight at age data,
##   0 rows of 'TAG1' comp data, and
##   0 rows of 'TAG2' comp data.
## Finished dimensioning
## You skipped the covar file
## Finished primary run statistics list
## 
## Statistics shown below (to turn off, change input to printstats=FALSE)
## $SS_version
## [1] "3.30.16.00;_2020_09_03;_safe;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_12.2"
## 
## $SS_versionshort
## [1] "3.30"
## 
## $SS_versionNumeric
## [1] 3.3
## 
## $StartTime
## [1] "StartTime: Wed Jul 21 10:33:46 2021"
## 
## $RunTime
## [1] "0 hours, 5 minutes, 13 seconds."
## 
## $Files_used
## [1] "Data_File: init_dat.ss Control_File: control.ss"
## 
## $Nwarnings
## [1] 8
## 
## $warnings
##  [1] "#V3.30.16.00;_2020_09_03;_safe;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_12.2"                                                                  
##  [2] "#Stock Synthesis (SS) is a work of the U.S. Government and is not subject to copyright protection in the United States."                                   
##  [3] "#Foreign copyrights may apply. See copyright.txt for more information."                                                                                    
##  [4] "Wed Jul 21 10:33:45 2021"                                                                                                                                  
##  [5] ""                                                                                                                                                          
##  [6] "settle_month is less than spawn_month, so logical age at settlement calculated to be: 1  for settle_time 1.  Does not match read value of 0 are you sure? "
##  [7] "setting in starter does not request all priors, and 5 parameters have priors and are not estimated, so their prior not included in obj_fun."               
##  [8] "Final gradient: 0.00238829 is larger than final_conv: 1e-05"                                                                                               
##  [9] " adjusted selparm out of base parm bounds (Phase, Iter, Parm#, yr, min, max, base, value) 6 967 13 1987 -10 15 8.36935 17.7371"                            
## [10] " adjusted selparm out of base parm bounds (Phase, Iter, Parm#, yr, min, max, base, value) 6 967 13 1988 -10 15 8.36935 17.7371"                            
## [11] " adjusted selparm out of base parm bounds (Phase, Iter, Parm#, yr, min, max, base, value) 6 967 13 1987 -10 15 8.36935 17.7371"                            
## [12] " adjusted selparm out of base parm bounds (Phase, Iter, Parm#, yr, min, max, base, value) 6 967 13 1988 -10 15 8.36935 17.7371"                            
## [13] "Number_of_active_parameters_on_or_near_bounds: 3"                                                                                                          
## [14] " N warnings: 8"                                                                                                                                            
## 
## $likelihoods_used
##                            values lambdas
## TOTAL                1999.2400000      NA
## Catch                   0.0169003      NA
## Equil_catch             0.0000000      NA
## Survey                -31.1208000      NA
## Length_comp          1016.9500000      NA
## Age_comp              906.1670000      NA
## Recruitment            23.9418000       1
## InitEQ_Regime           0.0000000       0
## Forecast_Recruitment    0.1936790       1
## Parm_priors             0.0000000       1
## Parm_softbounds         0.0510629      NA
## Parm_devs              83.0382000       1
## Crash_Pen               0.0000000       1
## 
## $likelihoods_laplace
##                                       values lambdas
## NoBias_corr_Recruitment(info_only)   23.9418       1
## Laplace_obj_fun(info_only)         1999.2400      NA
## 
## $likelihoods_by_fleet
##               Label          ALL   MexCal_S1   MexCal_S2         PNW AT_Survey
## 180    Catch_lambda           NA   1.0000000 1.00000e+00 1.00000e+00   1.00000
## 181      Catch_like    0.0169003   0.0168907 2.46461e-11 9.67905e-06   0.00000
## 182 Init_equ_lambda           NA   0.0000000 0.00000e+00 0.00000e+00   1.00000
## 183   Init_equ_like    0.0000000   0.0000000 0.00000e+00 0.00000e+00   0.00000
## 184     Surv_lambda           NA   0.0000000 0.00000e+00 0.00000e+00   1.00000
## 185       Surv_like  -31.1208000   0.0000000 0.00000e+00 0.00000e+00  -7.27937
## 186      Surv_N_use           NA   0.0000000 0.00000e+00 0.00000e+00  23.00000
## 187     Surv_N_skip           NA   0.0000000 0.00000e+00 0.00000e+00   0.00000
## 188   Length_lambda           NA   1.0000000 1.00000e+00 1.00000e+00   1.00000
## 189     Length_like 1016.9500000 278.7870000 4.59803e+02 1.63591e+02 114.77400
## 190    Length_N_use           NA  30.0000000 3.40000e+01 1.70000e+01   9.00000
## 191   Length_N_skip           NA   0.0000000 0.00000e+00 1.20000e+01   0.00000
## 192      Age_lambda           NA   1.0000000 1.00000e+00 1.00000e+00   1.00000
## 193        Age_like  906.1670000 193.7000000 3.64017e+02 2.12135e+02 136.31600
## 194       Age_N_use           NA 289.0000000 4.41000e+02 1.63000e+02 106.00000
## 195      Age_N_skip           NA  29.0000000 3.30000e+01 1.60000e+01   9.00000
##         DEPM  TEP_all
## 180  1.00000   1.0000
## 181  0.00000   0.0000
## 182  1.00000   1.0000
## 183  0.00000   0.0000
## 184  1.00000   1.0000
## 185 -8.20715 -15.6342
## 186 13.00000  23.0000
## 187  0.00000   0.0000
## 188  0.00000   0.0000
## 189  0.00000   0.0000
## 190  0.00000   0.0000
## 191  0.00000   0.0000
## 192  0.00000   0.0000
## 193  0.00000   0.0000
## 194  0.00000   0.0000
## 195  0.00000   0.0000
## 
## $Parm_devs_detail
##     Index Phase MinYr MaxYr stddev Rho Like_devs Like_se       mean     rmse
## 199     1     4  1982  2019   0.01   0   18.0323       0 -0.0158261 0.974201
## 200     2     5  1982  2019   0.11   0   65.0059       0 -0.5356730 1.849690
## 
## $N_estimated_parameters
## [1] 275
## 
## $table_of_phases
## 
## -99  -6  -5  -4  -3  -2  -1   1   2   3   4   5   6 
##   1   2   3   2  10   4   3  38   6 130  56  38   7 
## 
## $estimated_non_dev_parameters
##                                             Value Phase    Min   Max
## L_at_Amin_Fem_GP_1                   10.132700000     3   3.00 30.00
## L_at_Amax_Fem_GP_1                   23.326300000     3  15.00 40.00
## VonBert_K_Fem_GP_1                    0.616584000     3   0.05  0.99
## CV_young_Fem_GP_1                     0.180989000     3   0.05  0.50
## CV_old_Fem_GP_1                       0.041245700     3   0.01  0.10
## SR_LN(R0)                            16.322700000     1   3.00 25.00
## SR_regime_BLK1repl_1980              -4.760540000     4 -15.00 15.00
## InitF_seas_2_flt_2MexCal_S2           5.001860000     1   0.00 14.00
## Size_inflection_MexCal_S1(1)         13.560500000     3   0.00 30.00
## Size_95%width_MexCal_S1(1)            1.975260000     3   0.00 10.00
## AgeSel_P1_MexCal_S1(1)                0.498526000     3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)                0.501577000     3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)               10.028700000     3 -10.00 15.00
## AgeSel_P4_MexCal_S1(1)                0.794342000     3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)               -1.388510000     3 -10.00 11.00
## AgeSel_P6_MexCal_S1(1)                0.610979000     3 -10.00 11.00
## AgeSel_P7_MexCal_S1(1)               -1.140710000     3 -10.00 11.00
## AgeSel_P8_MexCal_S1(1)               -1.241410000     3 -10.00 11.00
## AgeSel_P9_MexCal_S1(1)               -5.816460000     3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)                8.369350000     3 -10.00 15.00
## AgeSel_P3_MexCal_S2(2)                1.759270000     3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)                0.268068000     3 -10.00 11.00
## AgeSel_P5_MexCal_S2(2)               -0.793967000     3 -10.00 11.00
## AgeSel_P6_MexCal_S2(2)                0.411625000     3 -10.00 11.00
## AgeSel_P7_MexCal_S2(2)               -1.233660000     3 -10.00 11.00
## AgeSel_P8_MexCal_S2(2)               -0.217423000     3 -10.00 11.00
## AgeSel_P9_MexCal_S2(2)               -1.920890000     3 -10.00 11.00
## Age_inflection_PNW(3)                 9.798310000     4   0.00 10.00
## Age_95%width_PNW(3)                   1.168340000     4  -5.00 15.00
## AgeSel_P2_AT_Survey(4)                1.146160000     4   0.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1983  4.380830000     3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1985  4.391080000     3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1987  5.827630000     3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1989  2.918220000     3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1991  0.504110000     3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1993  5.578460000     3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1995 -2.538470000     3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1997 -1.156910000     3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1999 -4.582480000     3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2001 -3.100720000     3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2003 -2.225720000     3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2005 -2.350380000     3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2007 -3.355650000     3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2009  6.551200000     3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2011  3.735560000     3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2013 -4.721470000     3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1983 -0.375324000     3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1985  1.044390000     3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1987  0.065048600     3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1989  1.432350000     3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1991 11.805200000     3 -10.00 15.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1993 -1.101940000     3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1995  2.165550000     3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1997 -0.081507300     3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1999  0.862265000     3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2001 -0.741943000     3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2003 -1.277650000     3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2005 -1.301360000     3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2007  0.576038000     3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2009  0.009128510     3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2011  0.411197000     3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2013  0.345985000     3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1983 -6.791940000     3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1985 -6.577600000     3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1987 -2.003120000     3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1989  3.262670000     3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1991  2.089600000     3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1993  2.019210000     3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1995  1.330810000     3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1997 -0.759134000     3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1999 -1.015490000     3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2001  0.046350400     3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2003 -0.527423000     3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2005 -0.166169000     3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2007 -1.451590000     3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2009 -0.853352000     3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2011  1.089490000     3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2013 -0.360910000     3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1983 -1.887870000     3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1985 -1.419030000     3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1987  3.096990000     3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1989 -7.129140000     3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1991  0.171356000     3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1993 -7.113480000     3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1995 -4.154440000     3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1997 -0.474855000     3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1999 -1.364360000     3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2001 -3.152860000     3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2003 -0.663141000     3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2005 -1.515550000     3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2007 -6.377660000     3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2009 -4.068960000     3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2011 -1.662910000     3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2013  1.768640000     3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_1987   9.367740000     3 -10.00 15.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_1989  -6.529080000     3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_1991  -7.965270000     3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_1993  -7.817700000     3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_1995  -8.815180000     3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_1997  -7.937600000     3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_1999  -8.963000000     3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_2001  -9.838380000     3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_2003  -7.858780000     3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_2005  -8.985060000     3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_2007  -8.773230000     3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_2009  -8.321650000     3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_2011  -9.977730000     3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_2013  -5.785790000     3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_1987  -0.396588000     3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_1989  -2.070610000     3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_1991  -1.206140000     3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_1993  -2.305950000     3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_1995  -0.945957000     3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_1997  -2.031790000     3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_1999  -1.858030000     3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_2001  -1.818520000     3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_2003  -2.647180000     3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_2005  -3.004590000     3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_2007  -2.729860000     3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_2009  -4.279050000     3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_2011  -0.880619000     3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_2013  -0.975195000     3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_1987  -0.224743000     3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_1989   1.293600000     3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_1991   0.811333000     3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_1993  -1.221430000     3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_1995  -1.400710000     3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_1997  -0.099285200     3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_1999  -2.149930000     3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_2001  -1.676120000     3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_2003  -0.003437220     3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_2005  -0.845493000     3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_2007  -1.854010000     3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_2009  -0.217583000     3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_2011  -0.045884000     3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_2013  -0.942944000     3 -10.00 11.00
## Age_inflection_PNW(3)_BLK4repl_1999   2.524920000     4   0.00 10.00
## Age_inflection_PNW(3)_BLK4repl_2001   2.625380000     4   0.00 10.00
## Age_inflection_PNW(3)_BLK4repl_2003   1.912140000     4   0.00 10.00
## Age_inflection_PNW(3)_BLK4repl_2005   2.806140000     4   0.00 10.00
## Age_inflection_PNW(3)_BLK4repl_2007   3.711570000     4   0.00 10.00
## Age_inflection_PNW(3)_BLK4repl_2009   3.978920000     4   0.00 10.00
## Age_inflection_PNW(3)_BLK4repl_2011   2.560110000     4   0.00 10.00
## Age_inflection_PNW(3)_BLK4repl_2013   3.275700000     4   0.00 10.00
## AgeSel_P2_AT_Survey(4)_BLK2repl_2012  7.402270000     4   0.00  9.00
## AgeSel_P2_AT_Survey(4)_BLK2repl_2013  7.856880000     4   0.00  9.00
## AgeSel_P2_AT_Survey(4)_BLK2repl_2014  0.944888000     4   0.00  9.00
## AgeSel_P2_AT_Survey(4)_BLK2repl_2016  8.057620000     4   0.00  9.00
## AgeSel_P2_AT_Survey(4)_BLK2repl_2018  0.000444865     4   0.00  9.00
## AgeSel_P2_AT_Survey(4)_BLK2repl_2019  9.845330000     4   0.00 11.00
##                                              Init Status Parm_StDev
## L_at_Amin_Fem_GP_1                    8.000000000     OK          0
## L_at_Amax_Fem_GP_1                   26.719900000     OK          0
## VonBert_K_Fem_GP_1                    0.721427000     OK          0
## CV_young_Fem_GP_1                     0.164739000     OK          0
## CV_old_Fem_GP_1                       0.039694500     OK          0
## SR_LN(R0)                            15.351600000     OK          0
## SR_regime_BLK1repl_1980              -2.254580000     OK          0
## InitF_seas_2_flt_2MexCal_S2          10.000000000     OK          0
## Size_inflection_MexCal_S1(1)         14.004200000     OK          0
## Size_95%width_MexCal_S1(1)            2.002900000     OK          0
## AgeSel_P1_MexCal_S1(1)                1.000040000     OK          0
## AgeSel_P2_MexCal_S1(1)                0.837451000     OK          0
## AgeSel_P3_MexCal_S1(1)               -0.884887000     OK          0
## AgeSel_P4_MexCal_S1(1)               -0.635305000     OK          0
## AgeSel_P5_MexCal_S1(1)                0.918160000     OK          0
## AgeSel_P6_MexCal_S1(1)               -0.111484000     OK          0
## AgeSel_P7_MexCal_S1(1)               -0.989063000     OK          0
## AgeSel_P8_MexCal_S1(1)               -1.493050000     OK          0
## AgeSel_P9_MexCal_S1(1)               -1.895360000     OK          0
## AgeSel_P2_MexCal_S2(2)                0.769735000     OK          0
## AgeSel_P3_MexCal_S2(2)                0.135819000     OK          0
## AgeSel_P4_MexCal_S2(2)               -0.104782000     OK          0
## AgeSel_P5_MexCal_S2(2)               -1.034120000     OK          0
## AgeSel_P6_MexCal_S2(2)                0.213999000     OK          0
## AgeSel_P7_MexCal_S2(2)               -1.773900000     OK          0
## AgeSel_P8_MexCal_S2(2)               -0.285435000     OK          0
## AgeSel_P9_MexCal_S2(2)               -6.978780000     OK          0
## Age_inflection_PNW(3)                 5.000950000     OK          0
## Age_95%width_PNW(3)                   0.483799000     OK          0
## AgeSel_P2_AT_Survey(4)                0.000433815     OK          0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1983  0.837451000     OK          0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1985  0.837451000     OK          0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1987  0.837451000     OK          0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1989  0.837451000     OK          0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1991  0.837451000     OK          0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1993  0.837451000     OK          0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1995  0.837451000     OK          0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1997  0.837451000     OK          0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1999  0.837451000     OK          0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2001  0.837451000     OK          0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2003  0.837451000     OK          0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2005  0.837451000     OK          0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2007  0.837451000     OK          0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2009  0.837451000     OK          0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2011  0.837451000     OK          0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2013  0.837451000     OK          0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1983 -0.884887000     OK          0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1985 -0.884887000     OK          0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1987 -0.884887000     OK          0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1989 -0.884887000     OK          0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1991 -0.884887000     OK          0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1993 -0.884887000     OK          0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1995 -0.884887000     OK          0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1997 -0.884887000     OK          0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1999 -0.884887000     OK          0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2001 -0.884887000     OK          0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2003 -0.884887000     OK          0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2005 -0.884887000     OK          0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2007 -0.884887000     OK          0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2009 -0.884887000     OK          0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2011 -0.884887000     OK          0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2013 -0.884887000     OK          0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1983 -0.635305000     OK          0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1985 -0.635305000     OK          0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1987 -0.635305000     OK          0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1989 -0.635305000     OK          0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1991 -0.635305000     OK          0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1993 -0.635305000     OK          0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1995 -0.635305000     OK          0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1997 -0.635305000     OK          0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1999 -0.635305000     OK          0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2001 -0.635305000     OK          0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2003 -0.635305000     OK          0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2005 -0.635305000     OK          0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2007 -0.635305000     OK          0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2009 -0.635305000     OK          0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2011 -0.635305000     OK          0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2013 -0.635305000     OK          0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1983  0.918160000     OK          0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1985  0.918160000     OK          0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1987  0.918160000     OK          0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1989  0.918160000     OK          0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1991  0.918160000     OK          0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1993  0.918160000     OK          0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1995  0.918160000     OK          0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1997  0.918160000     OK          0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1999  0.918160000     OK          0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2001  0.918160000     OK          0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2003  0.918160000     OK          0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2005  0.918160000     OK          0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2007  0.918160000     OK          0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2009  0.918160000     OK          0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2011  0.918160000     OK          0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2013  0.918160000     OK          0
## AgeSel_P2_MexCal_S2(2)_BLK7add_1987   0.769735000     OK          0
## AgeSel_P2_MexCal_S2(2)_BLK7add_1989   0.769735000     OK          0
## AgeSel_P2_MexCal_S2(2)_BLK7add_1991   0.769735000     OK          0
## AgeSel_P2_MexCal_S2(2)_BLK7add_1993   0.769735000     OK          0
## AgeSel_P2_MexCal_S2(2)_BLK7add_1995   0.769735000     OK          0
## AgeSel_P2_MexCal_S2(2)_BLK7add_1997   0.769735000     OK          0
## AgeSel_P2_MexCal_S2(2)_BLK7add_1999   0.769735000     OK          0
## AgeSel_P2_MexCal_S2(2)_BLK7add_2001   0.769735000     LO          0
## AgeSel_P2_MexCal_S2(2)_BLK7add_2003   0.769735000     OK          0
## AgeSel_P2_MexCal_S2(2)_BLK7add_2005   0.769735000     OK          0
## AgeSel_P2_MexCal_S2(2)_BLK7add_2007   0.769735000     OK          0
## AgeSel_P2_MexCal_S2(2)_BLK7add_2009   0.769735000     OK          0
## AgeSel_P2_MexCal_S2(2)_BLK7add_2011   0.769735000     LO          0
## AgeSel_P2_MexCal_S2(2)_BLK7add_2013   0.769735000     OK          0
## AgeSel_P3_MexCal_S2(2)_BLK7add_1987   0.135819000     OK          0
## AgeSel_P3_MexCal_S2(2)_BLK7add_1989   0.135819000     OK          0
## AgeSel_P3_MexCal_S2(2)_BLK7add_1991   0.135819000     OK          0
## AgeSel_P3_MexCal_S2(2)_BLK7add_1993   0.135819000     OK          0
## AgeSel_P3_MexCal_S2(2)_BLK7add_1995   0.135819000     OK          0
## AgeSel_P3_MexCal_S2(2)_BLK7add_1997   0.135819000     OK          0
## AgeSel_P3_MexCal_S2(2)_BLK7add_1999   0.135819000     OK          0
## AgeSel_P3_MexCal_S2(2)_BLK7add_2001   0.135819000     OK          0
## AgeSel_P3_MexCal_S2(2)_BLK7add_2003   0.135819000     OK          0
## AgeSel_P3_MexCal_S2(2)_BLK7add_2005   0.135819000     OK          0
## AgeSel_P3_MexCal_S2(2)_BLK7add_2007   0.135819000     OK          0
## AgeSel_P3_MexCal_S2(2)_BLK7add_2009   0.135819000     OK          0
## AgeSel_P3_MexCal_S2(2)_BLK7add_2011   0.135819000     OK          0
## AgeSel_P3_MexCal_S2(2)_BLK7add_2013   0.135819000     OK          0
## AgeSel_P4_MexCal_S2(2)_BLK7add_1987   0.135819000     OK          0
## AgeSel_P4_MexCal_S2(2)_BLK7add_1989   0.135819000     OK          0
## AgeSel_P4_MexCal_S2(2)_BLK7add_1991   0.135819000     OK          0
## AgeSel_P4_MexCal_S2(2)_BLK7add_1993   0.135819000     OK          0
## AgeSel_P4_MexCal_S2(2)_BLK7add_1995   0.135819000     OK          0
## AgeSel_P4_MexCal_S2(2)_BLK7add_1997   0.135819000     OK          0
## AgeSel_P4_MexCal_S2(2)_BLK7add_1999   0.135819000     OK          0
## AgeSel_P4_MexCal_S2(2)_BLK7add_2001   0.135819000     OK          0
## AgeSel_P4_MexCal_S2(2)_BLK7add_2003   0.135819000     OK          0
## AgeSel_P4_MexCal_S2(2)_BLK7add_2005   0.135819000     OK          0
## AgeSel_P4_MexCal_S2(2)_BLK7add_2007   0.135819000     OK          0
## AgeSel_P4_MexCal_S2(2)_BLK7add_2009   0.135819000     OK          0
## AgeSel_P4_MexCal_S2(2)_BLK7add_2011   0.135819000     OK          0
## AgeSel_P4_MexCal_S2(2)_BLK7add_2013   0.135819000     OK          0
## Age_inflection_PNW(3)_BLK4repl_1999   5.000950000     OK          0
## Age_inflection_PNW(3)_BLK4repl_2001   5.000950000     OK          0
## Age_inflection_PNW(3)_BLK4repl_2003   5.000950000     OK          0
## Age_inflection_PNW(3)_BLK4repl_2005   5.000950000     OK          0
## Age_inflection_PNW(3)_BLK4repl_2007   5.000950000     OK          0
## Age_inflection_PNW(3)_BLK4repl_2009   5.000950000     OK          0
## Age_inflection_PNW(3)_BLK4repl_2011   5.000950000     OK          0
## Age_inflection_PNW(3)_BLK4repl_2013   5.000950000     OK          0
## AgeSel_P2_AT_Survey(4)_BLK2repl_2012  0.000433815     OK          0
## AgeSel_P2_AT_Survey(4)_BLK2repl_2013  0.000433815     OK          0
## AgeSel_P2_AT_Survey(4)_BLK2repl_2014  0.000433815     OK          0
## AgeSel_P2_AT_Survey(4)_BLK2repl_2016  0.000433815     OK          0
## AgeSel_P2_AT_Survey(4)_BLK2repl_2018  0.000433815     LO          0
## AgeSel_P2_AT_Survey(4)_BLK2repl_2019  0.000433815     OK          0
##                                              Gradient  Pr_type Prior Pr_SD
## L_at_Amin_Fem_GP_1                    0.0004129400000 No_prior    NA    NA
## L_at_Amax_Fem_GP_1                    0.0003641360000 No_prior    NA    NA
## VonBert_K_Fem_GP_1                    0.0001858540000 No_prior    NA    NA
## CV_young_Fem_GP_1                     0.0000552808000 No_prior    NA    NA
## CV_old_Fem_GP_1                       0.0000248393000 No_prior    NA    NA
## SR_LN(R0)                             0.0023882900000 No_prior    NA    NA
## SR_regime_BLK1repl_1980               0.0007875360000 No_prior    NA    NA
## InitF_seas_2_flt_2MexCal_S2          -0.0000261434000 No_prior    NA    NA
## Size_inflection_MexCal_S1(1)          0.0000460351000 No_prior    NA    NA
## Size_95%width_MexCal_S1(1)            0.0000252338000 No_prior    NA    NA
## AgeSel_P1_MexCal_S1(1)               -0.0000004409960 No_prior    NA    NA
## AgeSel_P2_MexCal_S1(1)               -0.0000002487060 No_prior    NA    NA
## AgeSel_P3_MexCal_S1(1)                0.0000002844490 No_prior    NA    NA
## AgeSel_P4_MexCal_S1(1)                0.0000184525000 No_prior    NA    NA
## AgeSel_P5_MexCal_S1(1)               -0.0000017911000 No_prior    NA    NA
## AgeSel_P6_MexCal_S1(1)                0.0000582053000 No_prior    NA    NA
## AgeSel_P7_MexCal_S1(1)                0.0000115176000 No_prior    NA    NA
## AgeSel_P8_MexCal_S1(1)                0.0000050345500 No_prior    NA    NA
## AgeSel_P9_MexCal_S1(1)               -0.0000010454100 No_prior    NA    NA
## AgeSel_P2_MexCal_S2(2)                0.0000752276000 No_prior    NA    NA
## AgeSel_P3_MexCal_S2(2)                0.0000779974000 No_prior    NA    NA
## AgeSel_P4_MexCal_S2(2)                0.0000552218000 No_prior    NA    NA
## AgeSel_P5_MexCal_S2(2)                0.0000582164000 No_prior    NA    NA
## AgeSel_P6_MexCal_S2(2)                0.0001039840000 No_prior    NA    NA
## AgeSel_P7_MexCal_S2(2)                0.0001265330000 No_prior    NA    NA
## AgeSel_P8_MexCal_S2(2)               -0.0000093906300 No_prior    NA    NA
## AgeSel_P9_MexCal_S2(2)                0.0000032698200 No_prior    NA    NA
## Age_inflection_PNW(3)                 0.0000097495200 No_prior    NA    NA
## Age_95%width_PNW(3)                  -0.0000574965000 No_prior    NA    NA
## AgeSel_P2_AT_Survey(4)               -0.0000018101200 No_prior    NA    NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1983 -0.0000004753150 No_prior    NA    NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1985 -0.0000004489450 No_prior    NA    NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1987 -0.0000004658210 No_prior    NA    NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1989 -0.0000007346270 No_prior    NA    NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1991  0.0000004124690 No_prior    NA    NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1993 -0.0000000743509 No_prior    NA    NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1995 -0.0000067762900 No_prior    NA    NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1997 -0.0000035103600 No_prior    NA    NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1999  0.0003424160000 No_prior    NA    NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2001  0.0002928440000 No_prior    NA    NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2003  0.0000030969400 No_prior    NA    NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2005  0.0000156595000 No_prior    NA    NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2007  0.0001062260000 No_prior    NA    NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2009  0.0000001089530 No_prior    NA    NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2011 -0.0000000100571 No_prior    NA    NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2013  0.0000032174100 No_prior    NA    NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1983 -0.0000114249000 No_prior    NA    NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1985 -0.0000026537000 No_prior    NA    NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1987  0.0000132896000 No_prior    NA    NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1989 -0.0000004882750 No_prior    NA    NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1991  0.0000000213025 No_prior    NA    NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1993 -0.0000079205500 No_prior    NA    NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1995  0.0000068543200 No_prior    NA    NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1997  0.0000184488000 No_prior    NA    NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1999  0.0003720230000 No_prior    NA    NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2001  0.0001919990000 No_prior    NA    NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2003  0.0000095309500 No_prior    NA    NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2005  0.0000168828000 No_prior    NA    NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2007  0.0001017960000 No_prior    NA    NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2009  0.0000232025000 No_prior    NA    NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2011  0.0000023466900 No_prior    NA    NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2013  0.0000041264500 No_prior    NA    NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1983 -0.0000003705730 No_prior    NA    NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1985  0.0000000278957 No_prior    NA    NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1987  0.0000184008000 No_prior    NA    NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1989 -0.0000010338500 No_prior    NA    NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1991  0.0000003182380 No_prior    NA    NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1993 -0.0000029134700 No_prior    NA    NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1995  0.0000339261000 No_prior    NA    NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1997  0.0000268911000 No_prior    NA    NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1999  0.0000919447000 No_prior    NA    NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2001  0.0001267910000 No_prior    NA    NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2003  0.0000173136000 No_prior    NA    NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2005  0.0000152684000 No_prior    NA    NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2007  0.0000336254000 No_prior    NA    NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2009  0.0000349591000 No_prior    NA    NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2011  0.0000017603500 No_prior    NA    NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2013 -0.0000036137100 No_prior    NA    NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1983  0.0000011660300 No_prior    NA    NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1985  0.0000007834760 No_prior    NA    NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1987  0.0000163781000 No_prior    NA    NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1989 -0.0000000621945 No_prior    NA    NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1991 -0.0000030903100 No_prior    NA    NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1993 -0.0000003400530 No_prior    NA    NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1995 -0.0000084814300 No_prior    NA    NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1997  0.0000160585000 No_prior    NA    NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1999  0.0000267475000 No_prior    NA    NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2001  0.0000368947000 No_prior    NA    NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2003  0.0000113444000 No_prior    NA    NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2005 -0.0000044314700 No_prior    NA    NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2007  0.0000006995080 No_prior    NA    NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2009  0.0000006160660 No_prior    NA    NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2011  0.0000151818000 No_prior    NA    NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2013  0.0000048618900 No_prior    NA    NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_1987  -0.0000005176920 No_prior    NA    NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_1989  -0.0000052980600 No_prior    NA    NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_1991   0.0000370974000 No_prior    NA    NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_1993   0.0000017766200 No_prior    NA    NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_1995   0.0000133862000 No_prior    NA    NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_1997  -0.0000018761500 No_prior    NA    NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_1999   0.0000073162300 No_prior    NA    NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_2001   0.0000218295000 No_prior    NA    NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_2003   0.0000213894000 No_prior    NA    NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_2005   0.0000121440000 No_prior    NA    NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_2007  -0.0000137342000 No_prior    NA    NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_2009  -0.0000722672000 No_prior    NA    NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_2011   0.0000003970010 No_prior    NA    NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_2013   0.0000112483000 No_prior    NA    NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_1987  -0.0000106226000 No_prior    NA    NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_1989   0.0000228550000 No_prior    NA    NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_1991   0.0001138560000 No_prior    NA    NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_1993   0.0000180892000 No_prior    NA    NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_1995   0.0000194009000 No_prior    NA    NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_1997   0.0000019083700 No_prior    NA    NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_1999   0.0000034075200 No_prior    NA    NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_2001   0.0000201722000 No_prior    NA    NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_2003   0.0000114949000 No_prior    NA    NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_2005   0.0000014433000 No_prior    NA    NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_2007  -0.0000091310600 No_prior    NA    NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_2009  -0.0000746595000 No_prior    NA    NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_2011   0.0000049297700 No_prior    NA    NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_2013  -0.0000024032300 No_prior    NA    NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_1987  -0.0000499170000 No_prior    NA    NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_1989  -0.0000113576000 No_prior    NA    NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_1991   0.0000739941000 No_prior    NA    NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_1993   0.0000007493920 No_prior    NA    NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_1995   0.0000050113600 No_prior    NA    NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_1997  -0.0000024915200 No_prior    NA    NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_1999  -0.0000002018530 No_prior    NA    NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_2001   0.0000043343500 No_prior    NA    NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_2003   0.0000101805000 No_prior    NA    NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_2005  -0.0000151087000 No_prior    NA    NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_2007  -0.0000112271000 No_prior    NA    NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_2009  -0.0000986508000 No_prior    NA    NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_2011   0.0000218388000 No_prior    NA    NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_2013  -0.0000215378000 No_prior    NA    NA
## Age_inflection_PNW(3)_BLK4repl_1999   0.0000181743000 No_prior    NA    NA
## Age_inflection_PNW(3)_BLK4repl_2001   0.0000164624000 No_prior    NA    NA
## Age_inflection_PNW(3)_BLK4repl_2003   0.0000060034900 No_prior    NA    NA
## Age_inflection_PNW(3)_BLK4repl_2005   0.0000206243000 No_prior    NA    NA
## Age_inflection_PNW(3)_BLK4repl_2007   0.0000005837640 No_prior    NA    NA
## Age_inflection_PNW(3)_BLK4repl_2009  -0.0000105866000 No_prior    NA    NA
## Age_inflection_PNW(3)_BLK4repl_2011  -0.0000100990000 No_prior    NA    NA
## Age_inflection_PNW(3)_BLK4repl_2013  -0.0000289703000 No_prior    NA    NA
## AgeSel_P2_AT_Survey(4)_BLK2repl_2012  0.0000007567080 No_prior    NA    NA
## AgeSel_P2_AT_Survey(4)_BLK2repl_2013  0.0000005972430 No_prior    NA    NA
## AgeSel_P2_AT_Survey(4)_BLK2repl_2014 -0.0000001253380 No_prior    NA    NA
## AgeSel_P2_AT_Survey(4)_BLK2repl_2016  0.0000003886190 No_prior    NA    NA
## AgeSel_P2_AT_Survey(4)_BLK2repl_2018 -0.0000008999260 No_prior    NA    NA
## AgeSel_P2_AT_Survey(4)_BLK2repl_2019 -0.0000000386986 No_prior    NA    NA
##                                      Pr_Like Afterbound
## L_at_Amin_Fem_GP_1                        NA         OK
## L_at_Amax_Fem_GP_1                        NA         OK
## VonBert_K_Fem_GP_1                        NA         OK
## CV_young_Fem_GP_1                         NA         OK
## CV_old_Fem_GP_1                           NA         OK
## SR_LN(R0)                                 NA         OK
## SR_regime_BLK1repl_1980                   NA         OK
## InitF_seas_2_flt_2MexCal_S2               NA         OK
## Size_inflection_MexCal_S1(1)              NA         OK
## Size_95%width_MexCal_S1(1)                NA         OK
## AgeSel_P1_MexCal_S1(1)                    NA         OK
## AgeSel_P2_MexCal_S1(1)                    NA         OK
## AgeSel_P3_MexCal_S1(1)                    NA         OK
## AgeSel_P4_MexCal_S1(1)                    NA         OK
## AgeSel_P5_MexCal_S1(1)                    NA         OK
## AgeSel_P6_MexCal_S1(1)                    NA         OK
## AgeSel_P7_MexCal_S1(1)                    NA         OK
## AgeSel_P8_MexCal_S1(1)                    NA         OK
## AgeSel_P9_MexCal_S1(1)                    NA         OK
## AgeSel_P2_MexCal_S2(2)                    NA         OK
## AgeSel_P3_MexCal_S2(2)                    NA         OK
## AgeSel_P4_MexCal_S2(2)                    NA         OK
## AgeSel_P5_MexCal_S2(2)                    NA         OK
## AgeSel_P6_MexCal_S2(2)                    NA         OK
## AgeSel_P7_MexCal_S2(2)                    NA         OK
## AgeSel_P8_MexCal_S2(2)                    NA         OK
## AgeSel_P9_MexCal_S2(2)                    NA         OK
## Age_inflection_PNW(3)                     NA         OK
## Age_95%width_PNW(3)                       NA         OK
## AgeSel_P2_AT_Survey(4)                    NA         OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1983      NA         OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1985      NA         OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1987      NA         OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1989      NA         OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1991      NA         OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1993      NA         OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1995      NA         OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1997      NA         OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1999      NA         OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2001      NA         OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2003      NA         OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2005      NA         OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2007      NA         OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2009      NA         OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2011      NA         OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2013      NA         OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1983      NA         OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1985      NA         OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1987      NA         OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1989      NA         OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1991      NA         OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1993      NA         OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1995      NA         OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1997      NA         OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1999      NA         OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2001      NA         OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2003      NA         OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2005      NA         OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2007      NA         OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2009      NA         OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2011      NA         OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2013      NA         OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1983      NA         OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1985      NA         OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1987      NA         OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1989      NA         OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1991      NA         OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1993      NA         OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1995      NA         OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1997      NA         OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1999      NA         OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2001      NA         OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2003      NA         OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2005      NA         OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2007      NA         OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2009      NA         OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2011      NA         OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2013      NA         OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1983      NA         OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1985      NA         OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1987      NA         OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1989      NA         OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1991      NA         OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1993      NA         OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1995      NA         OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1997      NA         OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1999      NA         OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2001      NA         OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2003      NA         OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2005      NA         OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2007      NA         OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2009      NA         OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2011      NA         OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2013      NA         OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_1987       NA         OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_1989       NA         OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_1991       NA         OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_1993       NA         OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_1995       NA         OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_1997       NA         OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_1999       NA         OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_2001       NA         OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_2003       NA         OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_2005       NA         OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_2007       NA         OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_2009       NA         OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_2011       NA         OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_2013       NA         OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_1987       NA         OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_1989       NA         OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_1991       NA         OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_1993       NA         OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_1995       NA         OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_1997       NA         OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_1999       NA         OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_2001       NA         OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_2003       NA         OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_2005       NA         OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_2007       NA         OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_2009       NA         OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_2011       NA         OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_2013       NA         OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_1987       NA         OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_1989       NA         OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_1991       NA         OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_1993       NA         OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_1995       NA         OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_1997       NA         OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_1999       NA         OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_2001       NA         OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_2003       NA         OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_2005       NA         OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_2007       NA         OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_2009       NA         OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_2011       NA         OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_2013       NA         OK
## Age_inflection_PNW(3)_BLK4repl_1999       NA         OK
## Age_inflection_PNW(3)_BLK4repl_2001       NA         OK
## Age_inflection_PNW(3)_BLK4repl_2003       NA         OK
## Age_inflection_PNW(3)_BLK4repl_2005       NA         OK
## Age_inflection_PNW(3)_BLK4repl_2007       NA         OK
## Age_inflection_PNW(3)_BLK4repl_2009       NA         OK
## Age_inflection_PNW(3)_BLK4repl_2011       NA         OK
## Age_inflection_PNW(3)_BLK4repl_2013       NA         OK
## AgeSel_P2_AT_Survey(4)_BLK2repl_2012      NA         OK
## AgeSel_P2_AT_Survey(4)_BLK2repl_2013      NA         OK
## AgeSel_P2_AT_Survey(4)_BLK2repl_2014      NA         OK
## AgeSel_P2_AT_Survey(4)_BLK2repl_2016      NA         OK
## AgeSel_P2_AT_Survey(4)_BLK2repl_2018      NA      CHECK
## AgeSel_P2_AT_Survey(4)_BLK2repl_2019      NA         OK
## 
## $maximum_gradient_component
## [1] 0.00238829
## 
## $parameters_with_highest_gradients
##                                          Value    Gradient
## SR_LN(R0)                            16.322700 0.002388290
## SR_regime_BLK1repl_1980              -4.760540 0.000787536
## L_at_Amin_Fem_GP_1                   10.132700 0.000412940
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1999  0.862265 0.000372023
## L_at_Amax_Fem_GP_1                   23.326300 0.000364136
## 
## $Length_Comp_Fit_Summary
##      Factor Fleet Recommend_var_adj #  N Npos min_Nsamp max_Nsamp mean_Nsamp_in
## 2032      4     1          0.245368 # 30   30         1        89       24.9333
## 2033      4     2          0.419685 # 34   34         3       277       60.1765
## 2034      4     3          0.149375 # 29   17         1       174       80.0588
## 2035      4     4          0.837299 #  9    9        12        31       19.8889
##      mean_Nsamp_adj mean_Nsamp_DM DM_theta mean_effN HarMean_effN Curr_Var_Adj
## 2032        24.9333            NA       NA   31.2711      6.11783            1
## 2033        60.1765            NA       NA   56.9383     25.25510            1
## 2034        80.0588            NA       NA  109.6040     11.95880            1
## 2035        19.8889            NA       NA   22.7379     16.65300            1
##      Fleet_name
## 2032  MexCal_S1
## 2033  MexCal_S2
## 2034        PNW
## 2035  AT_Survey
## 
## $Age_Comp_Fit_Summary
##      Factor Fleet Recommend_var_adj # Nsamp_adj Npos min_Nsamp max_Nsamp
## 3128      5     1                 1 #        30  289         1     28.80
## 3129      5     2                 1 #        34  441         1     31.00
## 3130      5     3                 1 #        29  163         1     55.60
## 3131      5     4                 1 #         9  106         1      9.32
##      mean_Nsamp_in mean_Nsamp_adj mean_Nsamp_DM DM_theta mean_effN HarMean_effN
## 3128       2.53052        2.95142            NA       NA  31.29410      2.12682
## 3129       3.94177        4.24771            NA       NA  35.17100      2.13534
## 3130       6.97374        7.27632            NA       NA  37.06180      2.65545
## 3131       1.39585        1.79962            NA       NA   7.55662      1.14225
##      Curr_Var_Adj Fleet_name
## 3128            1  MexCal_S1
## 3129            1  MexCal_S2
## 3130            1        PNW
## 3131            1  AT_Survey
## 
## $SBzero
## [1] 573115
## 
## $current_depletion
## [1] 0.1373049
## 
## $last_years_SPR
## [1] 0.534885
## 
## $SPRratioLabel
## [1] "1-SPR"
## 
## $sigma_R_in
## [1] 1
## 
## $sigma_R_info
##            period N_devs SD_of_devs Var_of_devs mean_SE mean_SEsquared
## 1            Main     36   1.093647    1.196064       0              0
## 2      Early+Main     42   1.080642    1.167786       0              0
## 3 Early+Main+Late     48   1.013388    1.026956       0              0
##   sqrt_sum_of_components SD_of_devs_over_sigma_R sqrt_sum_over_sigma_R
## 1               1.093647                1.093647              1.093647
## 2               1.080642                1.080642              1.080642
## 3               1.013388                1.013388              1.013388
##   alternative_sigma_R
## 1            1.093647
## 2            1.080642
## 3            1.013388
## 
## $rmse_table
##     ERA  N    RMSE RMSE_over_sigmaR mean_BiasAdj
## 1  main 36 1.07835          1.16284     0.900787
## 2 early  6 1.00177          1.00355     0.393099
## completed SS_output
SSplotComps(replist = outputSS, kind = "LEN")

SSplotComps(replist = outputSS, kind = "AGE") # nothing happens

# Try using r4ss supporting function
tmp <- SSMethod.TA1.8(fit = outputSS, type = "len", 
                      fleet = 4, fleetnames = outputSS[["FleetNames"]], datonly = FALSE, 
                                  printit = FALSE)

# doesn't show compositions by length

unique(outputSS[["lendbase"]]$Yr) # doesn't have data from projection years (2020-2024)
##  [1] 1982 1983 1985 1987 1988 1989 1990 1992 1993 1994 1995 1996 1997 1998 1999
## [16] 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014
## [31] 1981 1984 1986 1991 2015 2016 2017 2018 2019
FleetNames <- outputSS[["FleetNames"]]

# try using ss3sim::get_compfit
# RW: function doesn't exist in the package? but it's in the index...
# get_compfit(report.file = outputSS, name = "len_comp_fit_table")

# run_SSMSE uses expected values for OM catch, so use these in figs
# RW: 'lendbase' only has observed years from historical time series
# termLenComps <- outputSS[["lendbase"]] %>% filter(Fleet == which(FleetNames == "AT_Survey")) %>%
#                   select(Yr, Seas, Fleet, Bin, Exp)

# Plot terminal age and length comps for OM and EM by iteration
termLenComps <- data.frame()
termAgeComps <- data.frame()

for(i in c(2,4:9)){
  outputSS <- SS_output(dir = paste0( "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", 
                                     i, "/cohortGrowthOMandEM_EM_2024"),
                        dir.mcmc = NULL,
                        repfile = "Report.sso",
                        compfile = "CompReport.sso", verbose = FALSE, printstats = FALSE)
  
  EMLenComps <- outputSS[["batlen"]] %>% filter(Yr == 2024, Seas == 2, `Beg/Mid` == "B") %>%
                  pivot_longer(cols = c("6", "6.5", "7", "7.5", "8", "8.5", "9", "9.5", "10", "10.5", 
                                        "11", "11.5", "12", "12.5", "13", "13.5", "14", "14.5", "15", "15.5",
                                        "16", "16.5", "17", "17.5", "18", "18.5", "19", "19.5", "20", "20.5",
                                        "21", "21.5", "22", "22.5", "23", "23.5", "24", "24.5", "25", "25.5", 
                                        "26", "26.5", "27", "27.5", "28", "28.5", "29", "29.5", "30"),
                               names_to = "Bin", values_to = "Biomass") %>%
                  mutate(Bin = as.numeric(Bin),
                         model_run = "cohortGrowthOMandEM_EM_2024",
                         iteration = i)

  EMAgeComps <- outputSS[["batage"]] %>% filter(Yr == 2024, Seas == 2, `Beg/Mid` == "B") %>%
                  pivot_longer(cols = c("0", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10"),
                               names_to = "Age", values_to = "Biomass") %>%
                  mutate(Age = as.numeric(Age),
                         model_run = "cohortGrowthOMandEM_EM_2024",
                         iteration = i)
  
  OMoutputSS <- SS_output(dir = paste0( "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", 
                                       i, "/0_estimate_cohort_growh_OM"),
                          dir.mcmc = NULL,
                          repfile = "Report.sso",
                          compfile = "CompReport.sso", verbose = FALSE, printstats = FALSE)

  OMLenComps <- OMoutputSS[["batlen"]] %>% filter(Yr == 2024, Seas == 2, `Beg/Mid` == "B") %>%
                  pivot_longer(cols = c("6", "6.5", "7", "7.5", "8", "8.5", "9", "9.5", "10", "10.5", 
                                        "11", "11.5", "12", "12.5", "13", "13.5", "14", "14.5", "15", "15.5",
                                        "16", "16.5", "17", "17.5", "18", "18.5", "19", "19.5", "20", "20.5",
                                        "21", "21.5", "22", "22.5", "23", "23.5", "24", "24.5", "25", "25.5", 
                                        "26", "26.5", "27", "27.5", "28", "28.5", "29", "29.5", "30"),
                               names_to = "Bin", values_to = "Biomass") %>%
                  mutate(Bin = as.numeric(Bin),
                         model_run = "0_estimate_cohort_growh_OM",
                         iteration = i)
  OMAgeComps <- OMoutputSS[["batage"]] %>% filter(Yr == 2024, Seas == 2, `Beg/Mid` == "B") %>%
                  pivot_longer(cols = c("0", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10"),
                               names_to = "Age", values_to = "Biomass") %>%
                  mutate(Age = as.numeric(Age),
                         model_run = "0_estimate_cohort_growh_OM",
                         iteration = i)
  termAgeComps <- rbind(termAgeComps, EMAgeComps, OMAgeComps)
  termLenComps <- rbind(termLenComps, EMLenComps, OMLenComps)
}
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
# RW: no composition data for last year because none provided in 'sample_struct_list' for run_SSMSE()
ggplot(termLenComps, mapping = aes(x = Bin, y = Biomass)) +
  geom_col() +
  facet_grid(cols = vars(model_run), rows = vars(iteration))

ggplot(termAgeComps, mapping = aes(x = Age, y = Biomass)) +
  geom_col() +
  facet_grid(cols = vars(model_run), rows = vars(iteration))

Generalized functions applied to Self Test with AT only

Make some generalized functions to apply to different scenarios

bDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
          scenario = "cohortGrowthselftest",
          termYr = 2024, surveyInx = 4)
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## [[1]]

## 
## [[2]]
## Warning: Removed 182 rows containing missing values (geom_point).
## Warning: Removed 7 row(s) containing missing values (geom_path).

compDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
              scenario = "cohortGrowthselftest",
              termYr = 2024)
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## [[1]]

## 
## [[2]]

# pull recruitment from summary dq
recrDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
              scenario = "cohortGrowthselftest", termYr = 2024)
## [[1]]

## 
## [[2]]
## Warning: Removed 14 row(s) containing missing values (geom_path).

#TotCatch_ in ss_summary.sso? or outputSS[["catch"]]
# outputSS <- SS_output(
#   dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024",
#   dir.mcmc = NULL,
#   repfile = "Report.sso",
#   compfile = "CompReport.sso", verbose = FALSE, printstats = FALSE)
# 
# catSmry <- outputSS[["catch"]] %>% group_by(Yr) %>%
#               # summarize totoal catch within year
#               dplyr::summarize(obsCat = sum(Obs),
#                                expCat = sum(Exp))

catchDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
              scenario = "cohortGrowthselftest", termYr = 2024)
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## [[1]]

## 
## [[2]]
## Warning: Removed 14 rows containing missing values (geom_point).
## Warning: Removed 7 row(s) containing missing values (geom_path).

FmsyDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
              scenario = "cohortGrowthselftest", termYr = 2024)

#SmryBio_ in ss_summary.sso? or outputSS[["timeseries"]]
# these aren't equal. SpawnBio matches between these files, but not outputSS[["timeseries"]]$Bio_smry

# outputSS[["timeseries"]] %>% select(Yr, Era, Seas, Bio_smry, `SmryBio_SX:1_GP:1`, SpawnBio)

age1plusDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
                  scenario = "cohortGrowthselftest", termYr = 2024)
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/cohortGrowthOMandEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/cohortGrowthOMandEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/cohortGrowthOMandEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/cohortGrowthOMandEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/cohortGrowthOMandEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/cohortGrowthOMandEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/cohortGrowthOMandEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/cohortGrowthOMandEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/cohortGrowthOMandEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/cohortGrowthOMandEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/cohortGrowthOMandEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/cohortGrowthOMandEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/cohortGrowthOMandEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/cohortGrowthOMandEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/cohortGrowthOMandEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/cohortGrowthOMandEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/cohortGrowthOMandEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/cohortGrowthOMandEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/cohortGrowthOMandEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/cohortGrowthOMandEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/cohortGrowthOMandEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/cohortGrowthOMandEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/cohortGrowthOMandEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/cohortGrowthOMandEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/cohortGrowthOMandEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/cohortGrowthOMandEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/cohortGrowthOMandEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/cohortGrowthOMandEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/cohortGrowthOMandEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/cohortGrowthOMandEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## [[1]]

## 
## [[2]]

Self-test with acoustic-trawl and age and length comps specified in projection period

bDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
          scenario = "cohortGrowthself_compNsamp",
          termYr = 2024, surveyInx = 4)
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## [[1]]

## 
## [[2]]
## Warning: Removed 127 rows containing missing values (geom_point).
## Warning: Removed 27 row(s) containing missing values (geom_path).

compDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
              scenario = "cohortGrowthself_compNsamp",
              termYr = 2024, surveyInx = 4)
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## [[1]]

## 
## [[2]]

recrDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
              scenario = "cohortGrowthself_compNsamp", termYr = 2024)
## [[1]]

## 
## [[2]]
## Warning: Removed 8 row(s) containing missing values (geom_path).

catchDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
              scenario = "cohortGrowthself_compNsamp", termYr = 2024)
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## [[1]]

## 
## [[2]]
## Warning: Removed 10 rows containing missing values (geom_point).
## Warning: Removed 5 row(s) containing missing values (geom_path).

FmsyDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
              scenario = "cohortGrowthself_compNsamp", termYr = 2024)

age1plusDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
              scenario = "cohortGrowthself_compNsamp", termYr = 2024)
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/cohortGrowthOMandEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/cohortGrowthOMandEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/cohortGrowthOMandEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/cohortGrowthOMandEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/cohortGrowthOMandEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/cohortGrowthOMandEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/cohortGrowthOMandEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/cohortGrowthOMandEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/cohortGrowthOMandEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/cohortGrowthOMandEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/cohortGrowthOMandEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/cohortGrowthOMandEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/cohortGrowthOMandEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/cohortGrowthOMandEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/cohortGrowthOMandEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/cohortGrowthOMandEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/cohortGrowthOMandEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/cohortGrowthOMandEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/cohortGrowthOMandEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/cohortGrowthOMandEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/cohortGrowthOMandEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/cohortGrowthOMandEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/cohortGrowthOMandEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/cohortGrowthOMandEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/cohortGrowthOMandEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/cohortGrowthOMandEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## [[1]]

## 
## [[2]]

Test with AT and comp data and fixed parameter EM

bDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
          scenario = "cohortGrowth_compNsamp",
          termYr = 2024, surveyInx = 4)
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## [[1]]

## 
## [[2]]
## Warning: Removed 130 rows containing missing values (geom_point).
## Warning: Removed 100 row(s) containing missing values (geom_path).

compDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
              scenario = "cohortGrowth_compNsamp",
              termYr = 2024, surveyInx = 4)
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## [[1]]

## 
## [[2]]

recrDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
              scenario = "cohortGrowth_compNsamp", termYr = 2024)
## [[1]]

## 
## [[2]]
## Warning: Removed 105 row(s) containing missing values (geom_path).

catchDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
              scenario = "cohortGrowth_compNsamp", termYr = 2024)
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## [[1]]

## 
## [[2]]
## Warning: Removed 105 rows containing missing values (geom_point).
## Warning: Removed 100 row(s) containing missing values (geom_path).

FmsyDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
              scenario = "cohortGrowth_compNsamp", termYr = 2024)

age1plusDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
              scenario = "cohortGrowth_compNsamp", termYr = 2024)
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/cohortGrowthOMfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/cohortGrowthOMfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/cohortGrowthOMfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/cohortGrowthOMfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/cohortGrowthOMfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/cohortGrowthOMfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/cohortGrowthOMfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/cohortGrowthOMfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/cohortGrowthOMfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/cohortGrowthOMfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/cohortGrowthOMfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/cohortGrowthOMfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/cohortGrowthOMfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/cohortGrowthOMfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/cohortGrowthOMfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/cohortGrowthOMfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/cohortGrowthOMfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/cohortGrowthOMfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/cohortGrowthOMfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/cohortGrowthOMfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/cohortGrowthOMfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/cohortGrowthOMfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/cohortGrowthOMfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/cohortGrowthOMfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/cohortGrowthOMfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## [[1]]

## 
## [[2]]
## Warning: Removed 95 row(s) containing missing values (geom_path).

# Look at growth and selectivity parameters
# outputSS <- SS_output(dir = file.path("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
#                                       "cohortGrowth_compNsamp", 1, "0_estimate_cohort_growh_OM"),
#                       dir.mcmc = NULL,
#                       repfile = "Report.sso",
#                       compfile = "CompReport.sso", verbose = FALSE, printstats = FALSE)
# SS_plots(outputSS, plot = c(1, 2, 16, 17, 20, 25, 26))
# 
# outputEM <- SS_output(dir = file.path("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
#                                       "cohortGrowth_compNsamp", 1, "cohortGrowthOMfixedParamsEM_EM_2024"),
#                       dir.mcmc = NULL,
#                       repfile = "Report.sso",
#                       compfile = "CompReport.sso", verbose = FALSE, printstats = FALSE)
# SS_plots(outputEM, plot = c(1, 2, 16, 17, 20, 25, 26))

Constant growth OM with AT and comp data and fixed parameter EM

bDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM",
          scenario = "constGrowth_compNsamp",
          termYr = 2024, surveyInx = 4)
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## [[1]]

## 
## [[2]]
## Warning: Removed 176 rows containing missing values (geom_point).
## Warning: Removed 146 row(s) containing missing values (geom_path).

compDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM",
              scenario = "constGrowth_compNsamp",
              termYr = 2024, surveyInx = 4)
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## [[1]]

## 
## [[2]]

recrDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM",
              scenario = "constGrowth_compNsamp", termYr = 2024)
## [[1]]

## 
## [[2]]
## Warning: Removed 105 row(s) containing missing values (geom_path).

catchDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM",
              scenario = "constGrowth_compNsamp", termYr = 2024)
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## The supplied data file has 3 sections.  Using section = 1.
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of section 1 of data file complete. Final value = 999
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## [[1]]

## 
## [[2]]
## Warning: Removed 147 rows containing missing values (geom_point).
## Warning: Removed 140 row(s) containing missing values (geom_path).

FmsyDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM",
              scenario = "constGrowth_compNsamp", termYr = 2024)

age1plusDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM",
              scenario = "constGrowth_compNsamp", termYr = 2024)
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowthOMfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowthOMfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowthOMfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowthOMfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowthOMfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowthOMfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowthOMfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowthOMfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowthOMfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowthOMfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowthOMfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowthOMfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowthOMfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowthOMfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowthOMfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowthOMfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowthOMfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowthOMfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowthOMfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowthOMfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowthOMfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowthOMfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowthOMfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowthOMfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowthOMfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowthOMfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowthOMfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowthOMfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowthOMfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowthOMfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowthOMfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowthOMfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowthOMfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowthOMfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowthOMfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowthOMfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowth_test2_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## [[1]]

## 
## [[2]]
## Warning: Removed 133 row(s) containing missing values (geom_path).

Sample size test with cohort growth OM model

age1plusDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
                  scenario = "5pctAnnChangeNsamp10Model", termYr = 2028)
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## [[1]]

## 
## [[2]]
## Warning: Removed 190 row(s) containing missing values (geom_path).

age1plusDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
                  scenario = "5pctAnnChangeNsamp20Model", termYr = 2028)
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## [[1]]

## 
## [[2]]
## Warning: Removed 190 row(s) containing missing values (geom_path).

age1plusDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
                  scenario = "5pctAnnChangeNsamp40Model", termYr = 2028)
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## [[1]]

## 
## [[2]]
## Warning: Removed 190 row(s) containing missing values (geom_path).

age1plusDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
                  scenario = "5pctAnnChangeNsamp100Model", termYr = 2028)
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/0_estimate_cohort_growh_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## [[1]]

## 
## [[2]]
## Warning: Removed 190 row(s) containing missing values (geom_path).

Marginal compositions OM and fixed selectivity EM with high data quality

bDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM",
          scenario = "margComps_highDatQual",
          termYr = 2028, surveyInx = 4)
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## [[1]]

## 
## [[2]]
## Warning: Removed 10 rows containing missing values (geom_point).
## Warning: Removed 10 row(s) containing missing values (geom_path).

compDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM",
              scenario = "margComps_highDatQual",
              termYr = 2028, surveyInx = 4)
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## [[1]]

## 
## [[2]]

recrDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM",
              scenario = "margComps_highDatQual", termYr = 2028)
## [[1]]

## 
## [[2]]
## Warning: Removed 20 row(s) containing missing values (geom_path).

catchDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM",
              scenario = "margComps_highDatQual", termYr = 2028)
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Char version is  3.30 
## Numeric version is  3.3
## Running SS_readdat_3.30
## SS_readdat_3.30 - read version = 3.30
## use_meanbodywt (0/1): 0
## N_lbinspop:
## use_lencomp (0/1): 1
## N_lbins: 39
## N_agebins: 9
## use_MeanSize_at_Age_obs (0/1): 0
## N_environ_variables: 0
## Read of data file complete. Final value = 999
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
## [[1]]

## 
## [[2]]
## Warning: Removed 20 rows containing missing values (geom_point).
## Warning: Removed 10 row(s) containing missing values (geom_path).

FmsyDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM",
              scenario = "margComps_highDatQual", termYr = 2028)

age1plusDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM",
              scenario = "margComps_highDatQual", termYr = 2028)
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_init/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2020/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2021/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2022/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2023/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2024/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2025/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2026/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2027/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2028/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margComp_20210921_OM/ss.cor
## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
##      'Variances are 0.0 for first two elements, so do not write '
##   input 'covar' changed to FALSE.
## [[1]]

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